Best Accounting Software for Physiotherapists

Are you a self-employed physiotherapist tangled in managing finances and the administrative side of your service? Managing a spreadsheet, tracking costs, and chasing unpaid invoices is time-consuming and will exhaust you after a long day at work. But there is a way to transform this chaos into calm – an efficient accounting software.

As a solo physiotherapist, you have to manage multiple administrative tasks like bookkeeping, cash flow management, and profitability all at once. In this situation, an accounting program can make or break your experience and work efficiency.

There are hundreds of options to choose from, and trying each of them is impossible. Be ready because we have tried the top 30 accounting software and brought you the top 5 that’ll save you time, increase profitability, and make your administrative work error-free.

Our best tested picks

• Xero – Best For Comprehensive Financial Management With Healthcare Integrations
• FreshBooks – Best For Streamlined Invoicing For Patient-Focused Practices
• Zoho Books – Best All-In-One Solution For Growing Practices
• Moss – Best For Modern Expense Management
• Melio – Best For Simplified Payment Processing And Bill Management

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Xero

Starting at
$2.90 p/month

Expert review

4.5 / 5

• Free trial

Read more

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Freshbooks

Starting at
$6.30 p/month

Expert review

4.7 / 5

• Free trial

Read more

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Zoho

Starting at
$10 p/month

Expert review

4.3/ 5

• Free trial

Read more

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Moss

Starting at
$0 p/month

Expert review

4.2/ 5

• Free trial

Read more

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Melio

Starting at
$19 p/month

Expert review

4.1 / 5

• Free trial

Read more

These are the best accounting programs for Physiotherapists

Physiotherapy is a more professional job than any other, and it requires you to spend a lot of time and focus on your patients. This accounting software will save your energy and time. Some of these software are designed as all-in-one accounting solutions, while others need some integrations and focus on specific areas like EMR.

Here is our detailed selection criteria while selecting these programs:

• Ease of Use: As a physiotherapist, you spend a lot of time with patients, and you will burn out during your working hours. In addition, you don’t want a complex accounting system that takes up your free time. In our trials, ease of use has been a priority so that employed physiotherapists can easily operate it.
  
• Appointment Scheduling: Managing clients is another important aspect of jobs like physiotherapy. Within the programs or with integrations, you can sync revenue with services rendered and also track missed appointments and billable vs. non-billable sessions.
  
• Bookkeeping: Tracking expenses to determine profitability is important in any business or service and crucial to growth. Without proper bookkeeping, you might be losing a lot of money on unnecessary things that you wouldn’t even know about. These software provides robust spend tracking and report generation with advanced automation tools.
  
• Integrations: Integration capabilities in accounting software are essential. It might be possible that you need advanced features or features outside of the program; in this case, third-party integrations could help you. With over 100 third-party integrations, you can add specific software features to enhance your accounting efficiency.
  
• Pricing:  All these programs offer different membership tiers for self-employed individuals and enterprises. We have carefully checked the pricing structure of this software and will give a detailed description later in this article.
  
• Customer Support: Customer support can make or break your accounting experience. These software provides customer support with different channels, including phone, email, chat, and comprehensive knowledge bases tailored to service-based businesses.

Top 5 Accounting Programs for Physiotherapists

We’ve done a detailed deep dive into the following software. From their primary use cases to small features, we’ve tried to cover everything so you can make an informed investment in your accounting software.

1. Xero – Best For Comprehensive Financial Management With Healthcare Integrations
2. FreshBooks – Best For Streamlined Invoicing For Patient-Focused Practices
3. Zoho Books – Best All-In-One Solution For Growing Practices
4. Moss – Best For Modern Expense Management
5. Melio – Best For Simplified Payment Processing And Bill Management

#1 Xero – Best for comprehensive financial management with healthcare integrations

A solo physiotherapist has to manage multiple administrative tasks, from invoicing to spending tracking alone, and maintain a positive cash flow, which is very important. Xero is a cloud-based accounting program that provides deeper analytics into finances and allows for managing cash flow in real time.

Xero enables physiotherapists to automate tasks easily, such as repeating invoices, accounts receivable, and payable, and saving hours. The software also provides reporting features that gather information on business performance, such as service, patient data, and more, thus allowing the financial situation of the company to be enhanced.

Expert score 4.7

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Key Features

Invoicing

• Xero provides customizable invoices with the option to integrate a logo and brand name, creating a professional image for clients.
• You can create an instant quote and budget, which can be easily converted into an invoice after the service.
• An embedded payment link on the invoice helps you get payment directly through the invoice.
• You can create an automated recurring invoice for regular patients, which saves you both time and extra work.

Expense Tracking

• Xero provides an accurate time tracker for time-based services that records time spent on services and charges directly on the invoice.
• For spending tracking, you can link your bank account; the expense will be automatically logged and categorized.
• With OCR features, you fetch details from a receipt with a single snap.
• Bank reconciliation features help find transactions and keep records error-free.

Cash Flow Management

• Real-time cash flow management feature to stay ahead of your finances.
• You’ll receive an alert every time your cash flow dips below a specific threshold.
• Xero’s cash flow forecast helps you to know your cash position ahead of the season or any specific high-demand periods after analyzing the past records.
• Automated reminders on cash receivables and payables.

Integrations

• Xero allows integrations with over 1000 third-party apps.
• You can integrate top healthcare programs like Depty, timely, and Splose.
• Xero does not provide client scheduling, but with easy integrations, many scheduling apps can be integrated. 

Payments

• Multiple payment methods, such as credit card and debit card.
• You can automate payment by ACH Direct Debit with GoCardless.
• The program provides high security and strong encryption to save users from fraud.

Reports

• A detailed profitability dashboard gives you a view of your financial condition, including a profit and loss statement.
• Xero tracks depreciation on your assets, saving time for taxes.
• You can monitor the breakdown of costs, including areas that need improvement.
• Tax reports that show tax obligations can be obtained using Xero.

Key Benefits For Physiotherapists

• Professional invoicing helps physiotherapists create their brand image.
• Automated spend tracking features save a lot of time, which they could use to improve service quality.
• With Xero’s advanced cash flow tools, such as cash flow forecasts and real-time tracking,  physiotherapists will never run short on cash.
• No hassle of payment, as Xero provides multiple channels to accept payment.
• Xero’s mobile application generates instant invoices, quotes, and reports, helping you operate instantly.

Xero: Customer Support

• Live Support: Xero doesn’t provide phone support to users, especially during unpredictable power outages. If you face any issues or have questions, reach out for assistance through email or live chat.
• Xero Central: Xero has released a page specifically for help that has a wide range of themes.
• AI Support: Xero launches the JAX (Just Ask Xero), a generative chatbot for quick inquiries.

Pros and Cons

#2 FreshBooks – Best For Streamlined Invoicing For Patient-Focused Practices

FreshBooks is one of the best accounting software programs for businesses looking for simple and basic accounting features. The biggest highlight of the platform is its simple interface, which includes all the necessary accounting features like invoicing, costing, payroll, etc. A physiotherapist using accounting software would not have a problem operating the program because of its simplicity.

Expert score 4.5

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Furthermore, FreshBooks allows integration with various third-party applications, which makes the platform more attractive to those who need details about specific features. Additionally, the software is highly suitable for multiple client management with features like a client portal, project collaboration tools, and client-specific reporting.

Key Features

Patient Management

• Dedicated patient portals to keep track of receivables and expenses in a single place.
• This portal provides a chatting system, so you can keep clients updated about schedules and services.
• Within this portal, you can download key financial reports that help you analyze which client contributes more to your success.
• Automatic notification if the credit is due by the client.

Automate Billing

• FreshBooks automates medical billing processes, including insurance claims and patient payments.
• You can generate brand and logo-integrated invoices for better marketing and relationships.
• Recurring invoices save time as you don’t have to create an invoice from scratch every time.
• You can get paid sooner by integrating a payment link on the invoice.
• You can monitor every activity of the invoice when the customer receives or views it, and create an invoice immediately on the mobile application.

Expense Tracking

• You can connect your bank and credit cards to the program for automated expense tracking.
• FreshBooks allows you to fetch data from receipt scanning or email upload, saving you time spent on manual logging.
• With FreshBooks, you can quickly mark your expenses as billable, add a markup, and then automatically pull them onto an invoice for your client.
• Real-time and accurate time tracking for accurate invoicing, ensuring you get paid for every billable hour.

Analytic Reports

• FreshBooks provides real-time financial insights through comprehensive financial, expense analysis, and profitability.
• You can easily check all your key financial metrics in a single dashboard.
• These detailed reports will not only guide you through your financials but will also help in tax season.

Payments and Integrations

• FreshBooks offers multiple CRM integration options, including HubSpot, Capsule CRM, and Nocrm.io.
• It also provides multiple payment options like credit cards, Apple Pay, and bank transfers. ACH also connects to most major banks in the U.S.
• Automatic recording and invoice matching save you time when processing month-ends.
• Set an automatic reminder for payables and late payments.

Key Benefits for Physiotherapists

• Simple UI helps physiotherapists operate the software efficiently.
• Automated billing and invoice options help them save time.
• Physiotherapists can accurately track expenses and time to convert every billable minute.
• Automated expense tracking by connecting your bank and credit card helps you to track expenses easily.
• Physiotherapists can accept payments with FreshBooks’ multiple payment options.
• Physiotherapists can integrate the software with multiple CRM programs to provide dedicated management features for patients.

FreshBooks Customer Support

• Dedicated Support Staff Assistance: FreshBooks’ support team has a high rating in the public reviews on Trustpilot- 4.8/5.0. You can contact FreshBooks Support services through phone, email, and chat.
• Comprehensive Knowledge Base: FreshBooks provides an online knowledge base and webinars, offering users information and self-service support options.

Pros and Cons

#3 Zoho Books – Best All-In-One Solution For Growing Practices

Zoho Books is one of the leading programs in the entire Zoho Suite, known for its robust accounting features and ability to handle a massive workload. The software provides strong project management capabilities, which can be adapted for patient case management, allowing Physiotherapists to track treatment plans, associated costs, and outcomes.

Another great thing about Zoho Books is its integration capability with other programs in the Zoho Suite. For physiotherapists, integration with Zoho CRM or Zoho Books could seamlessly complete all the accounting processes with client management in a single place.

Expert score 4.3

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Key Features

Patient Management

• Zoho CRM is a top client management tool that can be easily integrated into the Zoho Book for managing regular clients.
• Physiotherapists can create their booking page with Zoho Bookings, a one-stop solution for appointments. 
• For each client, there is a dedicated portal that helps you connect to them and manage their finances.
• Every activity of the client, like viewing the invoice, will be given, so you dont have to chase for payments.

Work Automation

• Zoho Books allows you to automate repetitive tasks like payment reminders and email marketing, saving your precious time.
• You can customize workflow rules for specific tasks.
• Quotes and budgets can be easily converted into invoices with one click.
• You can automate the invoice for regular clients, saving the hassle of repetitive creation and sending.

Invoice and Expenses

• Among the competitors, Zoho Books provides the best customizable invoicing with over 16 templates to choose from.
• Customized invoices with a logo and company name help you create a brand image in consumers.
• Multilingual invoicing option for foreign clients.
• You can directly bill the client for the time tracked and ask for approval for the same.
• One-click link payment through the Zoho invoice itself.
• For better expense management, Zoho attaches bills, receipts, and credit notes to associated transactions.
• You can reduce work by creating recurring profiles for expenses that take place regularly

Payment

• Customers can pay via credit cards, debit cards, ACH transfers, and potentially other options offered by the specific gateway.
• Zoho allows users to receive payment in multiple currencies from foreign clients.
• You can quote with a partial payment option to keep your cash flow balanced.
• Once receivables are completed, the invoices will be marked paid automatically.

Reporting and Integrations

• You can download automated data key financial matrices like receivables, profit, expenses, etc.
• You can easily generate reports instantly to view your financial health.
• With the reporting tag, you can know which of your services are giving you more benefits.
• Zoho Books lets you generate tax reports depending on your country’s regulations.

Key Benefits for Physiotherapists

• Tech-savvy physiotherapists can code their own automation workflows to save time.
• Patient management portals help physiotherapists connect better and create a healthy relationship.
• Professional invoice generation with a multi-language option to create a better brand image.
• Top integration tools within the Zoho suite and with third-party apps.
• Detailed business analysis reports help physiotherapists understand their financial condition and areas of improvement.

Zoho Books: Customer Support

• Chatting System: You can resolve your small queries through live chatting and email support.
• Phone Support: You can contact customer support from 5 AM to 6 PM hours a day, Monday to Friday, to solve your query.
• Guides and code: There are various online resources, like videos and blogs. Additionally, in-house codes are also available to help less tech-savvy physiotherapists.

Pros and Cons

#4 Moss – Best For Modern Expense Management

Running your own physiotherapy clinic often means wearing multiple hats, including being the scheduler, bookkeeper, and business manager. Moss is designed to ease that load. It helps you stay on top of everything from clinic rent and equipment costs to CPD course fees and mileage for home visits, all while giving you a clearer picture of how your business is performing financially.

Expert score 4.2

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Key Features

Smarter Expense Tracking

• It’s built-in AI sorts your expenses automatically, so you don’t have to spend time doing it manually.
• You’ll get real-time insights into how much you’re spending per patient program, service type, or even clinic location.
• You can even issue prepaid virtual cards to support staff, keeping their spending within approved limits.
• Reconciliation is automatic—say goodbye to chasing receipts and doing end-of-month number crunching.

Secure and Simple Payments

• Payments go directly through your connected bank account—no third-party gateways, so no delays.
• Full transaction reports are available to send to your accountant or keep for your records.
• It supports instant SEPA and UK payments, so it would be great if your clinic were based in the EU or the UK.
• Plus, you can earn cashback on higher-volume card payments—something that adds up quickly in a busy clinic.

Seamless Workflow Integration

• Moss plays nicely with tools you may already be using, like Xero or FreshBooks.
• With two-way syncing, your reports stay updated across platforms—less duplication, more accuracy.
• E-invoicing lets you collect and pay invoices directly through Moss or your linked account, making your workflow smoother.

Key Benefits For Physiotherapists

• A detailed report by Moss gives you a clear, categorized view of your clinic’s financial health.
• Automates the boring stuff like reconciling receipts and tracking business expenses.
• Makes tax season easier—every expense is already sorted and recorded.
• It helps you visualize where your money is going, whether it’s reinvested in new tools or your own professional development.

Customer Support

• Phone & Email Support: Reach the Moss team Monday to Friday, 9 a.m. to 4 p.m.
• Help Center: Moss provides a dedicated help center where you can browse step-by-step guides and troubleshooting articles anytime.

Pros and Cons

#5 Melio – Best For Simplified Payment Processing And Bill Management

Managing a physiotherapy practice involves tracking supplier invoices, staff payments, room rentals, and equipment purchases in addition to patient care. Melio is a smart and efficient payment solution for physiotherapists looking to simplify financial workflows without needing full accounting software.

Expert score 4.1

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Melio’s payment automation and seamless integrations make it easier to manage your cash flow, pay vendors, and collect payments from patients on time and without stress.

Key Features

Hassle-Free Payments

• Melio helps save time by automating bill payments and offers no-cost ACH transfers, which are perfect for routine clinic expenses.
• It presents multiple payment options, so you can accept patient payments through multiple channels, such as credit card, bank transfer, or mailed check.
• If a vendor prefers paper checks instead of online methods, Melio prints and mails them for you at a minimal fee.
• You can generate personalized payment links that provide clients the option to choose between debit or credit cards.

Easy Accounting Integration

• Offers multiple accounting software integration options like FreshBooks, Xero, and Amazon Business.
• Melio automatically reads receipts, saving you the time spent on manual logging.
• The software tracks bills, manages approvals, and keeps you organized, reducing your dependence on an accountant for every small task.
• Carries out in-depth analysis of payment transactions, offering key observations into spending trends and outstanding payables.

Financial Reporting

• Detailed reports help you understand where your clinic spends the most, whether on supplies, rent, administrative costs, or equipment.
• Melio helps you monitor client payment behavior, identify late payments, and make strategic financial decisions.
• It provides a clear record of all income and expenses to simplify tax filing or accountant handovers.

Key Benefits For Physiotherapists

• Melio reduces the time you spend chasing payments or manually logging invoices, freeing you up to focus more on patients.
• Allows your patients to pay online via credit card or bank transfer, decreasing delays in payment and billing disputes.
• Melio simplifies your end-of-year financial reporting and deductions with clear transaction records and synced accounting integration.
• It allows you to control when payments are sent to vendors, so you can align outflows with incoming patient revenue.

Melio: Customer Support

• Premium Support: A friendly and responsive support team is available via email and chat to help you out with payment and setup-related queries.
• Help Centre: You can also browse through an extensive help library with articles tailored to small business owners and health practitioners.

Pros and Cons

Top 5 Accounting Applications for Physiotherapists: Comparison Table

Price Information Per Program

It’s very important for you to take into consideration the price of each accounting software when you are making your choice. The following are the details about the cost structures for each of the systems we have talked about. Prices are subject to change, so it is advisable that you visit the software provider’s website to confirm the latest information.

Xero Pricing

Xero uses a subscription-based pricing model. Plans include (USD per month):

Note: Xero offers a 30-day free trial.

FreshBooks Pricing

FreshBooks uses a subscription-based model. Plans include (USD/month, with 70% off for 4 months):

Note: FreshBooks offers a 30-day free trial and a 30-day money-back guarantee.

Zoho Books Pricing

Zoho uses a subscription-based model.

Plans include:

Note: Zoho offers a 14-day free trial for the Standard and Premium plans. Prices are exclusive of local taxes.

Moss

Moss uses a modular pricing structure, determined by the chosen spend modules and add-ons, as well as the volume of transactions.

• Moss offers a free option for Corporate Cards (up to 3 users) and Accounts Payable (up to 20 invoices per month). Eligibility verification may be required.
  
• Pricing is customized by choosing spend modules (Corporate Cards, Employee Reimbursements, Accounts Payable), add-ons (Advanced Controlling, Advanced Accounting, Procurement, ERP), and transaction volume.

Melio

Melio’s pricing is primarily focused on transactions. There are generally no fees to receive payments.

• Fees may apply for certain payment methods, such as instant transfers.

When evaluating the cost of accounting software, consider not only the subscription fee but also potential additional costs, such as:

• Fees for extra users
• Add-ons or integrations
• Transaction fees
• Support costs (if applicable)

It’s also a good idea to take advantage of free trials to test the software and see if it meets your needs before committing to a paid plan.

Without good accounting software, you’re missing out on money

Inadequate financial management impacts your physiotherapy practice’s profitability and growth potential. Without proper accounting software, many practice owners lose money in ways that could easily be prevented.

Expense Management: Poor expense tracking can lead to missed valuable tax deductions. Physiotherapists have numerous deductible expenses, including equipment purchases, continuing education costs, professional licensing fees, and home office expenses if you provide telehealth services.

Taxes: Disorganized record-keeping can lead to overlooking many tax deductions and unnecessarily paying more taxes. Additionally, a disorganized billing process can lead to delayed payments, forgotten invoices, and difficulties with insurance reimbursement claims, all of which negatively impact your cash flow.

Work Quality: Manual financial management is time-consuming and error-prone, which could significantly lower your work quality. The hours you spend on bookkeeping tasks could be better used treating patients, marketing your practice, or developing new service offerings.

Profitability: For self-employed physiotherapists, inadequate accounting practices aren’t just an administrative headache—it can seriously hurt your profits and long-term business sustainability. Without proper financial software, there’s a good chance you’re missing out on money in a bunch of important areas.

Without clear financial insights, you might miss out on opportunities to optimize your pricing, identify your most profitable services, or recognize trends in patient behavior that could inform business decisions.

Insight into the financial situation of your physiotherapy practice

Accounting software insights can transform your understanding of your business finances, helping you manage them better. Modern accounting solutions offer real-time visibility into your practice’s financial health, helping you make data-driven decisions that support sustainable business growth.

Using proper accounting software, physiotherapists can track key financial insights, such as understanding which treatment modalities generate the highest revenue, identifying seasonal patterns in patient volume and income, and tracking the profitability of different service offerings. With these insights, you may find out that manual therapy sessions have higher profit margins than equipment-based treatments or that some insurance providers pay you significantly more than others.

Accounting software also helps track important practice metrics, such as average revenue per patient, treatment completion rates, and the cost of acquiring new patients. Understanding these numbers allows you to set practical financial goals, plan for equipment purchases or practice expansion, and ensure your pricing remains competitive while maintaining profitability.

Product	Xero	FreshBooks	Zoho	Moss	Melio
Learn more	>>> Learn More	>>> Learn More	>>> Learn More	>>> Learn More	>>> Learn More
Free trail period	30 days	30 days	14 days	30 days	30 days
Starting price	$2.90 p/month	$6.30 p/month	$10 p/month	Free	$19 p/month
Mobile Accessibility	✓	✓	✓	✓	✓
Payments and Banking	✓	✓	✓	✓	✓
Integration options	✓	✓	✓	✓	✓
Rating	4.7 / 5	4.5 / 5	4.3 / 5	4.2 / 5	4.1 / 5

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Softwarepointer.com is a platform that was created from a lot of passion for the accountancy profession. Founder Mark Rosbergen started the platform with aim of helping people with their entrepreneurial questions, especially in the field of accounting. With more dan 20 years of experience in accountancy, entrepreneurs are helped every day tot move forward with their business. How? Offering solutions for all entrepreneurial issues in the form of comparison tools, templates, rich articles and tops! We help your company move forward.