Best Modern Accounting Tools for Health Clinics in 2023

Words by
Lorraine Wong
Written on
August 14, 2023
Last updated on
August 14, 2023

We're thrilled to introduce this guest blog post by our friends at Enkel.

Explore Enkel's expert insights on the latest accounting solutions designed to empower healthcare clinics with efficient and effective financial management strategies.

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Your health clinic's main priority is the health and wellness of your patients. And while important, bookkeeping and other financial operations and activities can feel overwhelming and disorganized when there are so many more important things to stay focused on. Fortunately, with the advancements in accounting software and technology, there are many tools that can make your financial operations and processes much easier to manage, and far more efficient.

What are the benefits of using modern accounting tools for health clinics?

Using modern accounting software provides numerous benefits for health clinics. One of the key advantages is efficient financial management. With advanced tools and features, healthcare organizations can easily track their income, expenses, and cash flow in real-time. This allows finance teams to make informed decisions and ensures the financial health of the clinic.

In addition, modern accounting software streamlines billing and invoicing processes. Instead of manually creating and sending invoices, the software automates these tasks, saving valuable time for clinic staff. This not only improves efficiency but also reduces the risk of errors and ensures accurate billing.

Another benefit is the real-time access to financial data. With cloud-based accounting software, healthcare organizations can securely access their financial information anytime and anywhere. This enables accountants and healthcare professionals to stay updated on the clinic's financial status, make data-driven decisions, and analyze financial trends.

Top Accounting Tools for Health Clinics

1. QuickBooks Online

If you're running a health clinic, you already know the importance of accountant accuracy and efficiency. While your clinic practice management system and/or EMR software may provide invoicing and billing capabilities, you still require accounting software to track vendor invoices, expenses, and to reconcile your bank and credit card accounts. QuickBooks Online is one of the top cloud-based accounting platforms available on the market. You can easily export sales and billing data from your practice management/EMR system and import it into QuickBooks Online regularly.

You can use QuickBooks Online to track expenses and import sales reports to get a more in-depth understanding of your profitability. You can also generate numerous reports like cash flow statements, profit and loss, balance sheets, sales tax reports, and payables listings. Plus, QuickBooks Online includes the functionality to build clinic budgets and perform budget-to-actual comparisons. For health startups, freelancers, and small practices appreciating real-time financial data access and proficient transaction accuracies, QuickBooks Online is an excellent choice.

2. Dext Prepare

Dext Prepare has established itself as one of the top accounting tools for health clinics in 2023. It is exceptional at tracking and managing your expenses. You can effortlessly capture snapshots of your invoices and receipts, and the tool automatically extracts all the important data. This will save you a considerable amount of time on data entry. Plus, since a photo of all your invoices is saved directly to the cloud, there is no need to save and store the physical invoice.

This software serves as a centralized platform for consolidating all invoices from your suppliers. This benefit can be particularly valuable for health clinics dealing with a multitude of suppliers for medicines, equipment, and services. It also stores all of your documents in the cloud, providing easy and instant access to all your files. This accessibility can be a crucial asset in the fast-paced environment of a health clinic.

In short, Dext Prepare brings efficiency, accuracy, and clarity to your clinic's financial management, making it a top choice for health clinics in 2023.

3. Plooto

Once you’ve recorded your invoices in your accounting software, the next step is to get them paid. Plooto helps streamline your payables process and allows you to schedule your payments to vendors in a simple manner. With your approval, Plooto sends the payments electronically which helps you better manage cash flow and keep track of exactly how much money is flowing through your clinic at different times of the month/year. It also helps you stay up-to-date on your payables listing. Once invoices are paid, Plooto reconciles the payment in your accounting software and keeps your payables current.

Plooto also reduces the need for cheque payments. Even if your suppliers are located abroad, it is considerably more efficient to make online payments via direct deposit to payee's bank accounts than writing and mailing cheques. It also reduces the potential for human error.

Perfect for clinics prioritizing efficient payable processes, Plooto easily fits into vector payment management dynamics.

4. Payworks

As a health clinic, you are obligated to withhold payroll deductions such as CPP, EI, and taxes from your full-time employees every month, but your independent contractors handle their own deductions. Since many practice management/EMR solutions don’t address your payroll function, you need a software program that can deal with this for you. Payworks is an excellent option.

Payworks is a cloud-based software program that can manage your payroll and automatically calculate and remit the deductions to CRA on your behalf. This minimizes the amount of manual work you need to do, and ensures that you always stay compliant with tax obligations.

Payworks has two modules that can help a clinic manage its payroll: Time and Attendance and Absence Management.

Clinics use Time and Attendance so that hourly people can enter their hours, with the manager approving the hours before they are paid. This is far better than a spreadsheet or other written documentation that many clinics use today. Yes, people can forget to clock out, but this should be caught by the manager and adjusted accordingly.

Do you have salaried people who accumulate vacation time? Do you have a system to track the accrued vacation balance? If not, consider using Payworks Absence Management. The “bank” of time will increase each pay period and will be reduced when the employee takes approved vacation time off. This brings transparency to the tracking process and eliminates the risk of disagreement.

Variable compensation can be tricky to manage and each clinic might choose to do things differently. At the end of the day, it’s recommended that you create PDFs of reports showing the amounts from your EMR that team members are being compensated on. Calculations for commissions should be done in a standard way, typically in a spreadsheet. They should be prepared and reviewed by two different people (perhaps the clinic manager and owner) to ensure accuracy.

How can modern accounting tools help with healthcare cost accounting?

Implementing a modern cost accounting approach in healthcare organizations is crucial for effective financial management. Modern accounting tools provide the necessary features to accurately calculate and analyze healthcare costs. This allows clinics to identify areas of inefficiency and make informed decisions to improve cost-effectiveness.

Automation plays a significant role in modern cost accounting. By automating the accounting process, healthcare organizations can reduce manual errors and ensure accurate cost calculations. This saves time and resources, allowing accountants to focus on more strategic tasks rather than data entry.

Moreover, modern accounting tools enable healthcare organizations to manage and analyze their cost data in real-time. This provides valuable insights into the financial aspects of patient care, allowing clinics to optimize their operations and allocate resources effectively.

How can accounting software help healthcare organizations comply with financial regulations?

Accounting software plays a vital role in helping healthcare organizations comply with financial regulations. It ensures that all financial processes and transactions adhere to healthcare finance regulations, minimizing the risk of non-compliance and potential penalties.

Generating accurate financial reports for audits is one of the key benefits of using accounting software. The software can automatically generate detailed financial reports, providing a clear overview of the clinic's financial performance and compliance status. This streamlines the auditing process and saves time and resources for healthcare organizations.

Moreover, accounting software automates data entry, reducing errors and improving data accuracy. This is crucial for maintaining financial compliance and ensuring the integrity of financial information. By automating data entry, healthcare organizations can also save time and allocate resources more effectively.

What are the key features to consider when choosing accounting software for health clinics?

When selecting accounting software for health clinics, there are several key features to consider:

1. Cloud-based for easy access and collaboration

It is essential to choose cloud-based accounting software for easy access and collaboration. Cloud-based solutions allow multiple users to access financial data simultaneously and securely, which is particularly important for healthcare organizations with multiple locations or remote staff. Collaboration is another advantage of cloud-based accounting tools. By enabling secure access to multiple users, these solutions facilitate shared decision making and improve communication. Also, network sharing and knowledge exchange become significantly smoother with cloud implementations

2. Integrated payroll and billing functionality

Integration with payroll systems is also crucial for seamless payroll management. The accounting software should be able to integrate with existing payroll systems to automate payroll calculations and ensure accurate and timely salary payments for staff.

3. Core accounting tools tailored for healthcare industry

Accounting tools specifically designed for the healthcare industry play an integral role in the financial health of a healthcare organization. The benefits these tools offer to the healthcare industry are significant—they simplify complex processes, meet strict compliance requirements, and increase access to essential data, thereby improving overall financial management practices.

4. Comprehensive financial reporting and analysis

Comprehensive financial reporting and analysis forms a crucial part of any accounting software for health clinics. Regular review and analysis of financial statements - including balance sheets, cash flows, statements of operations, and changes in net assets - offer detailed insights into the practice's financial state.


Having the right tools in your clinic helps you streamline your financial operations, giving you more free time to focus on what matters most - your patients.

If you’re looking for more ways to simplify your financial procedures and gain better insight into the health of your clinic, contact Enkel today. We can provide you with all the expertise and assistance you need to keep your books in order, freeing up your time and saving you money.


Thanks to the team at Enkel for your insights! Head over to their blog for more tips on bookkeeping and accounting.

Lorraine Wong
Lorraine Wong
Founder @ Cue North

Helping leaders build great organizations through processes and powerful digital experiences