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The Best Accounting Software for Pharmacy

The all-new Accounting Software from FreshBooks empowers you to spend less time and stress on your pharmacy’s bookkeeping.

FreshBooks makes my life so much easier. I wish I had this when I first started my business!”

Reviews Tell Our Story

4.5 stars

FreshBooks offers simple cloud-based accounting software to help your pharmacy business grow smarter and faster. It takes care of the financial health of your business so you can focus on the health and wellbeing of your clients. Get started today to send custom invoices, track your expenses and accept online payments. With award-winning customer service, help is always just a quick email or phone call away. FreshBooks offers seamless integrations to manage payroll and track inventory directly from your account. Time is valuable when you run a busy pharmacy. Sign up with FreshBooks to save an average of 16 hours each month.

Bookkeeping Software Built for Your Pharmacy

As a pharmacist, you look after the health of community members by counselling clients on their medication options. Let FreshBooks look after the health of your business with its all-in-one accounting solutions. Simplify all your bookkeeping needs, from creating professional invoices to tracking employees’ time, recording business expenses and managing payroll. FreshBooks gives important financial insights to help you take your pharmacy business to the next level.

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New and Improved

The all-new FreshBooks now supports double-entry bookkeeping, to get deeper business performance data and growth potential insights. It can help you plan for your pharmacy’s future and save you time and money during tax season. You can even invite your accountant to collaborate on your FreshBooks account at no extra cost so they can access reports and analyze your business data. Watch your pharmacy business grow faster than ever with advanced bookkeeping tools from FreshBooks.

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Save Time

Running a busy pharmacy doesn’t always allow for a 9 to 5 workday. You may spend late nights and early mornings advising clients and filling prescriptions. Achieve a better work-life balance with FreshBooks by automating accounting tasks that slow you down. Automatically organize expenses, track time and follow up with customers.

Look Professional

Your pharmacy provides important professional services to the local community. FreshBooks helps you wow clients with invoices that are every bit as professional as you are. Create sleek invoices and reports that reflect the unique branding and personality of your pharmacy business, so you always stand out from the crowd.

Get Paid Faster

Pharmacies need a steady cash flow to pay their expenses and cover payroll. FreshBooks makes it easier than ever for clients to pay their invoices, so you don’t have to waste time chasing down payments. Get paid 11 days faster with convenient payment solutions that work for your pharmacy and your clients.

FreshBooks Accounting Software Testimonial Videos

Invoicing Software and Time and Expense Tracking for Pharmacies

To be successful, pharmacists need to free up as much time as possible to spend with clients. FreshBooks cloud accounting software helps you get more face time with customers and spend less time tied to a desk. Create custom invoices in minutes that reflect your unique branding. Add a personalized thank-you note and send invoices directly from your account in a matter of moments. FreshBooks offers the accounting tools you need to easily manage your books. Automatically record business expenses by linking your business bank account and credit card. Easily record your employees’ work hours with simplified time tracking.

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Recurring Invoices

Invoicing isn’t the most exciting part of a pharmacist’s day, but it’s crucial for keeping your business’s finances in order. Luckily, FreshBooks accounting software makes the process quicker and easier with recurring invoicing. Send recurring bills to the loyal clients you invoice regularly. You can create a recurring profile in a few clicks and FreshBooks will automatically send the invoices for you, freeing up your team’s time for more important tasks.

Payroll Management

Simplify your payroll system using the FreshBooks Gusto app integration for prompt payments and happy employees. You can set a recurring pay schedule that suits the needs of your small business. Your payroll system will automatically deduct federal, state and local taxes so there are never any errors on employee paychecks. Employees can even download tax documents themselves.

Pharmaceutical Inventory Tracking

When you handle vital medications for members of the community, proper inventory management is key to ensuring you never run out of life-saving medicine. FreshBooks integrates seamlessly with the BarCloud app for a sophisticated inventory management system. With an automated record keeping program, you can say goodbye to time-consuming manual data entry and be assured that your products are always in stock.


Make the billing process as simple as possible for your pharmacy and your clients. FreshBooks accounting software allows you to set up billing schedules so your clients can pay for prescriptions automatically and securely by credit card, without having to think about it. Your clients save time and your pharmacy gets the financial security of knowing exactly when payments come in. It’s a win-win.

Award-Winning Customer Support

  • Help From Start to Finish: Our Support team is highly knowledgable and never transfers you to another department.
  • 4.8/5.0 Star Reviews: Yup, that’s our Support team approval rating across 120,000+ reviews
  • Global Support: We’ve got over 100 Support staff working across North America and Europe
Award-Winning Customer Support

Accounting App for Pharmacies that Offers Secure Online Payments

FreshBooks makes it easier than ever for busy pharmacies to get paid with simple, secure online payments. Clients can pay by credit card straight from an invoice with just a couple of quick clicks. With high-level encryption and first-class security, your customers don’t have to worry about payment protection. FreshBooks offers a transparent, affordable fee structure to remove the guesswork from online payments for pharmacies. Billing isn’t the best part of running a pharmacy business. Let FreshBooks online payments look after it for you.

FreshBooks Integrates with All Your
Favorite Apps

You can now customize your FreshBooks experience with a range of business-friendly apps.

See all Integrations

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Take control of your pharmacy’s accounting with the help of these integrations.

Choosing an Accounting Software for Your Pharmacy

You’d like to spend the bulk of your day addressing the needs of clients, but sometimes the accounting burdens of running a pharmacy get in the way. You need accounting software built for small businesses to minimize the workload for you and your employees. FreshBooks offers best-in-class accounting tools designed with your pharmacy in mind. Ditch the complicated calculations and time-consuming spreadsheets for a suite of products that works together to offer a streamlined accounting solution to help your pharmacy grow.

Advance Your Pharmacy with Double-Entry Accounting on FreshBooks

When it comes to accounting, you need an “over-the-counter” solution that makes managing your businesses finances simple and affordable. You don’t need an accountant in order to take control of your pharmacy’s numbers.

Isn’t it time to use a system that works?

That’s where FreshBooks comes in. We’re obsessed with giving pharmacy owners exactly what they need in order to manage their books with ease. That’s why our accounting software now includes double-entry accounting – an industry standard feature that helps you keep all of your debits and credits in check.

These new double-entry accounting features include:

  • Cost of Goods Sold
  • General Ledger
  • Trial Balance
  • Chart of Accounts
  • Accountant
  • Access
  • Bank Reconciliation
  • Bank Sheet
  • And Other Income

Never leave whether your pharmacy is “in the black” up to guess. With the the addition of double-entry accounting, you can manage your accounting professionally and effectively.

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What Is the Best Accounting App for a Pharmacy?

Running a busy pharmacy means you need to be able to do important work from anywhere. The FreshBooks mobile app lets you work on your business finances on the go, whether you’re running a report on the bus or tracking inventory while out of town for a conference. FreshBooks stays in sync across all your devices, so you always have access to the latest financial data. Upload receipts and respond to clients and vendors directly through the app, from wherever work takes you.

Accounting Software for Pharmacies Free Download

Get started using simple cloud-based accounting software for your pharmacy with a free 30-day trial. FreshBooks lets you test out its easy-to-use features for a full 30 days before committing — no strings attached and no fine print. You don’t even need a credit card number to get started.

Sign up for your free trial today to start growing your pharmacy business and managing your finances the easy way.


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