What is the Best Bookkeeping Software for Therapists? 7 Picks
Chances are, you went to grad school because you were excited to help people. Now, here you are, running a therapy practice that needs to juggle HIPAA compliance, insurance billing, self-pay clients, sliding scale fees, and a mountain of receipts from CEUs and supervision. Fun, right?
The right bookkeeping software can solve these headaches, saving you 10-15 hours a week on expense tracking, tax prep, and more. The wrong software — or worse, trying to DIY things in Google Sheets — can land you in a world of hurt with IRS penalties. But how can you identify the best bookkeeping software for therapists?
In this post, I'm breaking down seven bookkeeping software options with honest pros and cons for each. Some are free, some are comprehensive, and some try to do everything (spoiler: they don't always succeed). We'll talk about what they do well, where they fall short, and which one makes sense for your practice.
Why Therapists Need Specialized Bookkeeping Software
Running a therapy practice isn't like running a retail shop or consulting business. You're juggling stuff that most businesses never encounter. Let’s take a look at a few of the things that make therapy practice finances unique:
HIPAA compliance requirements: Your financial records can't expose client information, which means you need careful systems for tracking sessions without violating privacy laws.
Multiple payment streams: You have to juggle insurance reimbursements, self-pay clients, sliding scale fees, and EAP contracts.
Professional expenses: CEUs, supervision hours, licensure renewals, liability insurance, and professional memberships are all deductible, but you need to track them properly.
Session-based billing: You're not invoicing projects or selling products; you're billing by the hour across multiple clients with different rates and payment methods.
You’ll want to find a bookkeeping software solution that helps mitigate these challenges for your practice.
What to Look For in the Best Bookkeeping Software for Therapists
Before we dive into specific software recommendations, let's lay some groundwork for how I made this list. What makes a bookkeeping software solution a top option for therapy practices?
HIPAA compliance capabilities: Any system that touches client information needs proper safeguards, even if it's just tracking payment methods by client ID.
Integration with your practice management software: If your EHR and bookkeeping don't talk to each other, you're doing double data entry (and probably making mistakes).
Multiple payment method tracking: Cash, checks, credit cards, insurance payments, and HSA cards all need their own paper trail.
Expense categorization for therapy-specific costs: CEUs aren't office supplies, and your liability insurance isn't the same as general business insurance. You need a solution that allows you to categorize your expenses in a way that makes sense.
Tax prep support for Schedule C filers: Most therapists are sole proprietors or single-member LLCs, which means you have different tax reporting needs from an S-Corp or C-Corp.
Mobile access: Therapists often travel to conferences or work out of multiple office locations. You need to be able to track expenses on the spot wherever you are.
Solid bank reconciliation: This is non-negotiable for catching errors before they become expensive problems.
One final point before we get into the nitty-gritty of our list: Software is only as good as the data you put into it.
Even the best bookkeeping platform can't fix messy categorization or months of neglected entries. You’ll need to regularly categorize your expenses and track payments in your system consistently. Sometimes, the best bet is finding a CPA to take bookkeeping off your plate altogether, but more on that later.
Related Read: Do I Need a Bookkeeper? (+ How To Find the Right Partner)
#1: QuickBooks Online (QBO)
Best for: Growing or established therapy practices and anyone planning to work with a bookkeeper or CPA down the road
QuickBooks Online is my top pick for therapy practices. QBO is the industry standard in bookkeeping for good reason. And, since it is so standard, whenever you bring in a CPA, they’ll almost certainly know QuickBooks inside and out from day one.
Key features:
Bank reconciliation QBO connects directly to your bank and links transactions to your actual account balance.
Multiple cash flow reporting options: You can report direct and indirect methods. QuickBooks also handles things like depreciation correctly.
Tax prep integration: This tool works seamlessly with TurboTax, and your CPA can access your books remotely, making taxes smooth sailing.
Mobile receipt scanning: You can take photos of receipts anywhere you have internet connection, tracking expenses in real time.
Third-party integrations: Connects with SimplePractice (via export), payroll services, and hundreds of other tools.
Pricing: $25–$180/month depending on features (most therapists do fine with Simple Start at $25 or Essentials at $50)
There is a bit of a learning curve with QuickBooks. The software has a lot of features and, as a result, it has a lot of buttons. You might spend a few hours figuring it out (or work with a CPA who can help), but once you get set up you’ll have solid reporting and simple tracking.
#2: FreshBooks
Best for: Solo practitioners who want something simple and aren't planning major expansion
If QuickBooks feels like overkill and you mostly need to send invoices and track time, FreshBooks might be your speed. It’s a simple-to-use interface that most people pick up fairly quickly, which is a draw for some solo practitioners.
Key features:
Professional invoice templates with automated billing
Time tracking
Client portal
Expense tracking with receipt scanning
Pricing: FreshBooks’ Plus plan starts at $19 a month.
If you go with FreshBooks, you're trading simplicity for features. FreshBooks doesn't have the advanced accounting capabilities or the ecosystem of integrations that QBO offers. If your practice grows or you hire a bookkeeper, you might end up needing to migrate to something more robust.
#3: Xero
Best for: Group therapy practices where multiple people need to see the books
Xero’s claim to fame is its offer of unlimited users on most plans, which is rare. If you're in a group practice or planning to share access with a business partner, Xero makes collaboration pretty easy.
Key features:
Real-time bank feed connections
Automated transaction categorization
Strong reporting and analytics
No user limits on standard plans
Pricing: Plans range from $25-$90 per month
The challenge with Xero is that it formats its financial reports differently from what most accountants expect. The reports are simpler to read if you don't know accounting, but they're harder to share with professionals who do, so if you plan to work with a CPA down the road, this might pose a problem.
#4: Wave
Best for: Brand new therapists on a shoestring budget
Wave is appealing because it’s free. Actually free, not "free trial then pay" or "free but limited." Full double-entry bookkeeping, invoicing, and receipt scanning all with no charge.
Key features:
Complete accounting system at $0/month
Invoice creation and tracking
Receipt scanning and expense tracking
Basic reporting
The catch is that Wave makes money by charging fees when clients pay invoices via credit card (2.9% + $0.30) or bank transfer (1%). Wave also falls into the category of solutions that are fine for now, but will not be enough as you grow. That’s not necessarily a bad thing if you’re just starting out, but be prepared to migrate your data down the road.
Related Read: Small Business CPA Near Me: 7 Best Places To Find a Partner
#5: Zoho Books
Best for: Therapists already using another Zoho tool
If you're already using other Zoho products (CRM, email, etc.), Zoho Books is a solid choice because it’ll integrate with your existing tools.
Key features:
Project time tracking and billing
Client portal access
Automated workflows and reminders
Integration with the broader Zoho suite
Pricing: Zoho offers plans from $20-$70 per month
Outside of Zoho's world, integrations are limited. There aren't many healthcare-specific features, so if you’re not already in the Zoho ecosystem, I don’t know if I’d recommend this one for therapists.
#6: SimplePractice
Best for: Solo practitioners who don't need advanced accounting features
SimplePractice isn’t purely a bookkeeping solution; it’s practice management software that also includes billing features and basic financial tracking. This tool gives you scheduling, client notes, billing, and a client portal.
Key features:
Integrated client scheduling and billing
Insurance claim processing
Treatment plan and progress note integration
Basic financial reporting
Pricing: Plans range from $49-$99 per month.
SimplePractice is a solid billing tool, but the financial reporting is pretty basic. Many therapists using SimplePractice still need QuickBooks or similar accounting software for actual bookkeeping, tax prep, and understanding their profitability.
#7: TherapyNotes
Best for: Solo practitioners who don't need advanced accounting features
Like SimplePractice, TherapyNotes combines electronic health records with practice management and billing. If clinical documentation integration is your top priority, it's worth a look, but this is another solution you’ll probably outgrow on the accounting side.
Key features:
Electronic health records (EHR) system
Integrated scheduling and billing
Insurance verification and claim processing
Treatment planning and documentation
Basic financial reporting
Pricing: TherapyNotes’ Solo plan starts at $59 per month.
The bookkeeping features of TherapyNotes are basic. You're getting a great EHR and practice management system, but you'll likely still need dedicated accounting software (hello again, QuickBooks) for comprehensive financial management, expense tracking, and tax preparation.
Why the Best Bookkeeping Software for Therapists Needs the Right CPA Partner
QuickBooks is great. Wave is free. FreshBooks is easy to use. Whichever option you choose for your practice, there’s still one important consideration: none of them can protect you from expensive mistakes.
Even with the best bookkeeping software, it’s easy for a busy therapist to miscategorize an expense or miss deductions for things like CEUs, home office costs, or clinical supervision. You might forget to track mileage or get confused about quarterly estimated taxes and end up with penalties.
Ultimately, you need more than just the best bookkeeping software for therapists to keep your practice running smoothly. You need a CPA.
A CPA who specializes in health and wellness practices understands the unique expenses you deal with, from licensure renewals to professional liability insurance. They’ll do proactive tax planning throughout the year, not just reactive filing in April. And the right CPA will also actually respond to your emails. No "I sent three messages and heard nothing" experiences. You get monthly support, not a "see you next year" relationship.
The best bookkeeping software for therapists is ultimately the one paired with someone who knows how to use it for your practice. If you’re curious about how the right CPA can help manage your books and keep your business financials clean, book a free Discovery Call with me. I’ll look through your books and give you my advice on where to get started, whether we end up working together or not.
