Empower Your Practice

Journal for Practice Managers

6 Best Healthcare Payroll Software for Better Performance Management

Healthcare payroll software is designed to automate the payroll management process in the healthcare industry. It facilitates the handling of payroll payments and accounting for various financial aspects related to staff payroll.

Here are some of the main features that are commonly provided by healthcare payroll management software:

  • Timekeeping
  • Payroll calculation and deductions
  • Leave and sick leave management
  • Regulatory and legal compliance
  • Reporting and analytics.

The choice of HR software is huge.

On the Software Suggest website, a search for "payroll software for healthcare" brings up a list of 140 suggestions.

So how do you choose the right one for you?

We have done some of the work and will tell you about the best deals on workforce management software in English-speaking countries.

Every clinic must conduct a constant monitoring of key growth factors. Medesk facilitates payroll accounting and helps to track your employees’ working hours. Besides, we provide you with all the statistics you need to make payments in the required amount.

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1. Gusto


Gusto is an HR system, one of the main functions of which is the automation of payroll calculations.

The platform allows you to pay your employees as many times a month as necessary. The developers do not charge any additional fees. Gusto automatically fills and files payroll taxes, synchronising the hours of work of the team.

All necessary forms for HR specialists are stored and filled out online:

  • I-9;
  • W-2;
  • Contractor 1099 form;
  • Form 941, etc.

To free up time for important tasks, you can activate payroll on AutoPilot. This is an optional feature from Gusto that allows you to payroll automatically at a designated period.

Gusto has its own debit card that allows you to get simplified access to your payroll on a payday.

The platform offers advanced features as well:

  1. Payroll reports are used to analyse bank transfers, payments, and tax deductions.
  2. Integration with Receipt Bank.
  3. Automatic employee time tracking.
  4. Integration with Xero, QuickBooks, and FreshBooks.


Gusto offers three pricing plans: Simple, Plus, and Premium.


Prices start at $40 per month plus $6 per user.

If you run a contractor-only business, Gusto has a separate plan for you with a discounted base price of $0 per month for 6 months and an additional $6 per month per contractor.

2. ADP


This comprehensive payroll solution is widely used by many businesses. It offers services from human resources and payroll to benefits, talent, and compliance.

ADP has positioned itself as software that can serve both small businesses and corporations with 1000+ employees. You can work either on a computer or in a mobile app.

Key features:

  1. Autopilot payroll
  2. AI-powered payroll inspector to detect errors in receipts
  3. Employee time tracking.
  4. Full automation of tax payments.
  5. Maintain reporting for tax authorities.
  6. Self-service onboarding for employees.


ADP does not provide open information about the cost of services on its website. The price of the connection depends on the number of employees and the frequency of pay days and is announced after consultation.

According to some sources, the Essential Plan starts at $79 per month plus $4 per employee.


3. QuickBooks Payroll

This versatile payroll service integrates directly with QuickBooks' extensive accounting software.


The platform offers the following features:

  1. Same-day direct deposit. You can enter employee data on hours worked, PTO, or payroll. Salary checks will be automatically deposited on the day you pay salaries.
  2. Automated tax payment. Fill out the forms online. The platform will do the rest.
  3. Tax penalty protection. If you've received a tax penalty while working with QuickBooks, you'll be paid up to $25,000, which will help you resolve problems with the IRS.
  4. Time tracking. You can create schedules, approve time, track employees on shift, and create payroll planning reports.
  5. Integrations. QuickBooks supports integrations with ADP, Square, Gusto, Paychex, Dropbox, OnPay, etc.

The platform works with both small businesses (accountants) and medium- to large-sized companies, including healthcare practices.


QuickBooks has a total of four pricing plans:


The payroll option is added separately and costs from $22.5 to $62.5 per month, depending on the features and a plan.

For example, in the Essentials plan, the Payroll Core feature costs $22.5 per month and includes automated payroll and taxes, an employee portal, 401(k) plans, 1099 forms, etc. Other options are shown in the screenshot below.


4. Paycor

Known for its excellent customer service and versatile functionality.


The software offers the following features:

  1. OnDemand Pay. With Paycor, you can give your employees access to the money they earn before payday. The creators claim that the freedom to dispose of payments attracts and retains more talented people.
  2. Mobile Wallet. An app where employees can manage their benefits, request statements, use budget management tools, and direct bill payments.
  3. Autorun. Schedule payments in advance and enable automated deferred payments.
  4. Tax compliance. In the main menu of the programme, you will be able to see notifications about tax payments and changes in tax legislation.
  5. Automatic form filling. Paycor processes forms W-2, 1099, and tax filing.
  6. Reports. Payroll reports are generated in two clicks. DDS can analyse cash requirements, tax liabilities, and more.
  7. Employee self-service. Employees can access pay stubs on their own at any time with just a mobile phone.


Paycor works with businesses of all sizes. The cost is not publicly disclosed and depends on the number of employees in the company. You will need to contact the sales office to confirm the price.

However, the website has information about four tariff plans:


The Capterra website states that the plans start at $99 per month.

5. Staffology Payroll by IRIS

Offers full-featured cloud payroll and an API for businesses and bureaus.


Saffology offers its customers a set of features, including:

  1. Payroll automation. It includes autopilot abilities, payslip distribution, payments summary, and automated timesheets.
  2. API. You can push it into any type of software: accounting, practice management, attendance. Applications that can be integrated include Sage, Xero, Nest, CIPHR, and others. The Staffology API is recognised by His Majesty's Revenue and Customs.
  3. Accounting integration. After salaries are paid, it's time for accounting. Staffology integrates with KashFlow, Reckon One, AccountsIQ, QuickBooks, and others, so you can automatically create journal entries.
  4. Payroll for Scotland and Wales. Scotland and Wales set their own tax rates. The platform supports the legislation of both countries.
  5. Reports. Create P30, P32, and P11 reports and operational reports to analyse your business without leaving the platform.


The cost of an additional employee depends on the number of payslips created each month. The more employees, the lower the cost of additional payslips.

The minimum monthly payment is £10. There is a handy calculator on the website where you can calculate the cost of a subscription. For example, 50 payslips will cost £92.50 per month.


Please note, it is essential to choose the payroll software that best suits your business's specific needs. Each software solution listed offers a diverse range of features and tools that best serve different types of businesses.

Practice Management Software with Payroll Software Options

Direct payroll functionality may not be a standout feature of most medical practice management software. However, they usually provide compatibility or integration capabilities with other payroll processing tools, thereby seamlessly incorporating payroll functions into the system.

For many healthcare providers, the choice of a PMS with an additional payroll module will be preferable. For the same amount of money, they get more functionality for many HR tasks at once:

We will also tell you about PMS and the quality HR solutions inside.

Do you want to learn more? Leave a request for a Medesk demo access.

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6. Medesk

This practice management software provides professional HR tools for patient interaction, payrolls, and patient billing.


Medesk automatically tracks doctors' working hours, generates reports on amounts paid and days worked. Within the platform, you can split payments into fixed and bonus payments, create a reward system for clinicians and admin staff.


Medesk bonus calculations help you build a transparent system of rewards based on different parameters and the achievements of your employees:

  • bonuses for performed appointments, paid invoices;
  • different percentages of bonuses for different services rendered;
  • bonuses to the receptionist for the number of booked appointments and absence of no-shows.

We recommend using the analytics module reports to identify employee experiences worthy of reward and to strengthen your human capital management.


Medesk offers three tariffs: Mini, Pro, and Premium.


The payroll feature is available on the Pro plan for $28/month for 30+ features that cover all the needs of healthcare professionals.

Summing Up

Choosing the right healthcare payroll software is crucial if you want to streamline operations and ensure compliance within the healthcare sector. Making the right choice demands careful consideration of the specific needs and requirements of your organisation.

  1. Among the top contenders in the market, Gusto stands out for its user-friendly interface, automated payroll processing, and integration capabilities with popular accounting software.
  2. Meanwhile, ADP offers a comprehensive suite of services catering to businesses of all sizes, with features such as autopilot payroll and AI-powered error detection.
  3. QuickBooks Payroll provides seamless integration with its accounting software, along with same-day direct deposit and automated tax payments.
  4. Paycor offers innovative features like OnDemand Pay and a mobile wallet, ensuring flexibility and convenience for employees.
  5. If you are seeking a fully integrated solution, Staffology Payroll by IRIS offers cloud-based payroll automation, API integration, and specialised customer support for businesses operating in Scotland and Wales.
  6. Medesk stands out for its robust practice management tools, including advanced payroll features such as bonus calculations and comprehensive analytics.

The choice between a standalone payroll system and practice management systems with integrated payroll functionality depends on the unique needs and priorities of your healthcare organization.

You can find a detailed review of the top PMS on the market in our blog. We're analysing our competitors to help you make a thoughtful choice that will improve overall patient care.

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