Many churches have limited administrative staff and want a full-bodied payroll software that can automate payroll workflows, address payment and tax issues, and even assist staff with administering HR.

In other cases, church administrative organizations may assume payroll duties for a number of churches that are affiliated with them. In these cases, the church administrative organization is known as a professional employer organization that handles the payroll and even the HR functions for many smaller churches that are under its umbrella.

Because needs vary, these are some of the questions that church organizations should ask themselves when evaluating payroll systems:

  • Do you want someone to handle all of your payroll for you, or are you interested in doing your own payroll?
  • Do you function in multiple states and countries?
  • How important is it to have excellent customer support?
  • Is the payroll system easy to use and does it work well with your other systems?
  • Does the payroll system fit your budget?

Here are seven payroll systems worth considering.

2023: Best church payroll services

Feature Gusto Paychex Justworks ADP Rippling Papaya Paycor
Employee and contractor Payroll, direct deposit and essential payroll functionality Yes Yes Yes Yes Yes Yes Yes
PEO support No Yes Yes No Yes Yes No
Payroll service outsourcing No Yes Yes Yes No No No
Standalone payroll offering Yes Yes No Yes No No Yes
Payroll as part of HR suite Yes Yes Yes Yes Yes Yes Yes
Global payroll and multi-currency Yes No No Yes Yes Yes No

Gusto: Best for organizations that want to start small with payroll and scale up to HR

The Gusto logo.
Image: Gusto

First launched in 2012 as ZenPayroll, Gusto serves more than 200,000 businesses nationwide. It’s a great choice for smaller organizations because it can functionally scale beyond payroll. For example, Gusto also offers a complete suite of other HR integrated software such as talent management, 401(k) and retirement plan management, healthcare benefits, program development and support.

In short, Gusto can scale into being a “one-stop automated shop” for smaller organizations that can’t afford a large HR or payroll staff.


  • Offers self-service employee tools for both payroll and HR functions, such as sending out automatic notifications about open positions.
  • Comes with analytics and insights reporting that assists you in analyzing your workforce.
  • Offers assistance and guidance to organizations in selecting the best healthcare plans and benefits, based upon company profile.
  • Provides automatic software updates that assure clients have the latest compliance for payroll and benefits.
  • Comes with built-in checklists for onboarding new employees and enrolling them in payroll.
  • Has built-in integration with other third party applications.
  • Provides employer tax filing support.
  • Provides employee and contractor payroll (hourly and salaried).


  • Unlimited payroll runs for no extra charge.
  • State tax registration in all 50 states.
  • Local, state and federal payroll tax filing.
  • International contractor payments in over 80 countries.
  • Automatic tax calculations.
  • Time tracking synced with payroll.
  • Supports direct deposit.


  • Some flexibility limitations when it comes to defining payroll pay periods.
  • Clients report that customer support is inconsistent.
  • It can be difficult to streamline software workflows for speed if you don’t want to use all of the features.
  • May not be the best fit for seasonal businesses, as it can be difficult to pause operations.


  • Simple Plan: Payroll only plan at $40 per month plus $6 per month per person
  • Plus Plan: Integrated Payroll, Benefits and HR suite plan at $60 per month plus $9 per month per person
  • Exclusive Plan: Contains all of the functions of the Plus Plan plus vendor support. Pricing is determined per individual company.

Rippling: Best for organizations that want a totally integrated payroll and HR system

The Rippling logo.
Image: Rippling

Rippling offers HR Cloud, a complete HR package that provides payroll as one of its modules. Other modules include talent management, learning management (training), benefits, time and attendance, PEO software for employers that must manage and administer to smaller organizations, and employee surveys.

Rippling is best utilized by companies that want a total HR solution and/or are structured such that an overall enterprise is charged with running HR and payroll for multiple sub-organizations.


  • Global workforce management with multiple currency options for payroll.
  • Workflow automation for functions like onboarding new hires, and changing deductions.
  • Has a broad network of different providers and software with which it is readily integrated.
  • Employee self-service web portal.
  • Provides employer tax filing support.
  • Offers employee and contractor payroll (hourly and salaried).
  • Supports direct deposit.


  • A total, integrated HR package, so you get much more than payroll.
  • If you’re an enterprise that must manage and administer payroll and HR for multiple sub-organizations, Rippling is well suited for that.
  • Useful dashboards that are easy to navigate.
  • Integration between different modules of the system is very tight.
  • Supports local, state and federal tax filing and payments to employees and contractors in foreign countries.


  • Support staff is difficult to communicate with when you need immediate help.
  • The payroll module requires clients to configure their own setups and has limited reporting functions.
  • Updates to the product are continuous, which can make it hard to keep up.
  • Does not offer a standalone payroll software for companies that want that.


  • Pricing starts at $8 per month per user.

Paychex: Best for smaller organizations and PEOs that want strong regulatory compliance and client support options

The Paychex logo.
Image: Paychex

Paychex is a highly scalable payroll offering that can start as a fully outsourced payroll function for very small companies, and scale to a company-run payroll system that is fully integrated with an HR, insurance, healthcare and benefits, and retirement plan system for mid- to large-sized enterprises.


  • Contains both standard and analytics reporting.
  • Payroll and HR software are tightly integrated.
  • An employee self-service portal is included.
  • Paychex provides a mobile app for both employers and employees.
  • There is an online knowledge center to keep customers informed of new issues that impact compliance, taxes and payroll.
  • Employer tax filing is supported.
  • Employee and contractor payroll (hourly and salaried) is supported.
  • Supports direct deposit.


  • Places strong emphasis on regulatory compliance, which saves time for customers.
  • Offers an ecosystem of professional accountants, banking professionals and financial advisors who are available to organizations for consultation.
  • The user interface and the flow of the system are intuitive and easy to use.
  • Supports PEOs.
  • It’s easy to add new employees and modify existing employee information.
  • Payroll reports are comprehensive and easy to use.


  • While email support is 24/7, immediate customer support is not always available by phone or through chat.
  • Online training tools could be more robust.
  • Add-on software options are expensive for smaller organizations.
  • The login process is cumbersome.


  • Paychex Flex Essentials is $39 per month plus $5 per employee
  • Paychex Flex Select is priced on a per-company basis.
  • Paychex Flex Pro is priced on a per-company basis.

Justworks: Best for organizations that want to outsource all of their payroll to a PEO

The Justworks logo.
Image: Justworks

Justworks is a PEO that offers outsourced HR and payroll services and turnkey HR and Payroll software. Justworks is an ideal solution for organizations that don’t want the administrative burden of running their own payroll and HR, and want the assurance that someone with expertise and software in the payroll/HR area can do it for them.

If your organization is small, this could be a concierge-level offering that may be pricey, but if you are mid-sized or larger, this offering will help you focus on your core mission while an outside PEO handles HR and payroll for you.


  • Justworks offers full PEO services.
  • Payroll and payments are fully automated and paperless.
  • Employees have a self-service portal.
  • Employer tax filing support is provided.
  • Justworks processes both employee and contractor payroll (hourly and salaried).
  • Supports direct deposit.


  • As a PEO, Justworks joins together small- and medium-sized businesses into a single, larger buying group to achieve cost-savings for insurance and outside services.
  • Has 24/7 real person support via email, phone or chat.
  • Justworks does the payroll setup for you.
  • Has an HR consulting service.
  • Offers a mobile app.
  • Intuitive and easy to use interface.


  • JustWorks is expensive for very small companies.
  • Integration capabilities with other third party software could be more robust.
  • If ad hoc payments need to be made, the payment calendar can be somewhat inflexible.
  • Does not have e-signature functionality.


  • Basic version with payroll management, compliance support, HR training and HR management tools: $59 per month per employee.
  • Deluxe version with Basic offerings plus health insurance coverage, advanced reporting, company directory and accounting software integrations: $99 per month per employee.

Papaya: Best for organizations with multi-country and multi-currency needs

The Papaya Global logo.
Image: Papaya Global

Papaya is a cloud-based SaaS platform that offers integrated payroll, HR and workforce management. It is configured for use in over 160 countries. Papaya is a great fit for global companies that must administer payrolls, employees and contractors in multiple countries. It also supports PEOs.


  • Provides real-time reporting with BI and analytics.
  • Online employee self-service portal.
  • Automated workflows for approvals, user permissions and notifications.
  • Employer tax filing support.
  • Employee and contractor payroll (hourly and salaried).
  • Flexible deployment options: You can use web-based SaaS, or an in-house Windows, Mac or smartphone platform.
  • PEO support.
  • Supports direct deposit.


  • Strong compliance support, including a built-in accuracy and compliance engine that verifies payroll data before it’s processed.
  • Easy integration with other payroll and HR systems.
  • Strong customer support, and a dedicated account manager.
  • Flexible workflows and robust system security.
  • Access to compliance, legal and payroll experts.


  • Website navigation can be cumbersome.
  • System error recovery can be slow.
  • The HR module lacks learning management and performance review tools.
  • The system is expensive for smaller companies.


  • Payroll: $25 per month per employee.
  • Contractor management: $25 per month per person.
  • Employer of Record or PEO version: $650 per month per employee.

ADP: Best for organizations looking lots of options

The ADP logo.
Image: ADP

Originally started in 1949, ADP has been in the payroll processing business for decades. It began as a payroll servicing firm and later branched out into providing its own payroll software to companies.

Today, ADP clients still have a choice: They can outsource to ADP to perform all of their payroll functions, an attractive option for small companies, or they can opt to subscribe to ADP payroll software. ADP also has an option that combines payroll into a total HR offering. Companies can pick and choose depending upon their budgets and their goals.

If you’re not outsourcing your payroll functions to ADP, there are three different software packages and feature sets that ADP offers.

Essential payroll is a basic payroll offering that contains payroll processing, tax filing, an online employee portal, direct deposit and reporting.

Enhanced payroll includes all of the functionality of Essential payroll, and adds to it State Unemployment Insurance management, check signing and stuffing, garnishment payment services, labor law compliance and recruitment.

Complete Payroll & HR Plus includes all of the functionality of the Enhanced payroll package, and adds to it HR capabilities such as an employee handbook wizard, an HR help desk, new hire onboarding, HR forms and documents, HR compliance, HR tracking, alerts and notifications, a training module, an employee discount program and a secure document vault.


  • Three different software packages.
  • An online employee self-service portal is provided.
  • Supports direct deposit.


  • ADP is easily scalable, from basic payroll up to a fully integrated payroll-HR system.
  • The payroll systems provide detailed reports.
  • Payroll Is accessible from a plethora of desktop and mobile devices.
  • ADP integrates well with the other third party software.
  • Tax filings are automated.
  • A digital onboarding process renders getting new employees started on the HR side easy.
  • Payroll works in over 140 countries.


  • Can be pricey for small companies.
  • Some clients report experiencing system errors that have to be worked through or recomputed.
  • Since ADP offers so many features and configuration options, initial system setup and choices can be confusing.
  • Customer service is not always timely.
  • If you are a larger company looking for robust HR software, the ADP Payroll/HR combination may not be the best choice, as ADP’s core competence is payroll.


  • Pricing is done on a per-company basis.

Paycor: Best for organizations requiring tightly integrated payroll and HR

The Paycor logo.
Image: Paycor

Paycor offers a combination payroll and HR package that automates and assists in many areas of payroll processing while also leveraging employee-specific information from the HR system. Job profiles, organization structures and employee promotions can be tied to payroll related functions such as employee transfers, raises and payments.

The payroll-HR integration creates a holistic view of employees and what the company and its various organizations are paying for talent. Paycor is well suited for small and mid-sized organizations that want to tightly integrate their payroll and HR functions. There is also a Basic version of the software that offers payroll only.

Paycor comes in four versions: Basic is an elementary payroll and tax service that comes with OnDemand payments and Online Reporting. Essential includes everything in the basic plan and adds employee onboarding, time-off management and an HR Support Center. Core includes everything in the Essential plan and adds expense management, the ability to import employee information such as CSVs, the Paycor HR system and Paycor career management. Complete is a full suite of Paycor payroll and HR that comes with analytics, compensation planning and talent management.


  • Offers four versions.
  • Paycor supports employer tax filing.
  • Supports direct deposit.
  • The system provides employee and contractor payroll (hourly and salaried).
  • Automated workflows are available for employee transfers, promotions and pay raises.
  • Employee self-service portal.
  • Off-cycle and on demand payments can be processed.
  • Includes a set of pre-built reports and allows users to customize reports.
  • The Paycor Complete system provides analytics.


  • Integrates well with other third party applications.
  • The system is easy to navigate.
  • Has built-in compliance data.
  • Provides a payroll auditing function that checks for payroll accuracy.
  • All payroll and HR information is visible and consolidated into one area of the system, which simplifies research and administration.


  • Clients report that customer support is weak.
  • Implementation can be difficult.
  • Employee self-service portal occasionally fails.


  • Basic plan: $99 per month plus $5 per employee per month.
  • Core plan: $199 per month plus $8 per employee per month.

Choosing the right payroll software

Payroll services and software is a mature field, so the good news is that almost every payroll system will have the basic functionality you need. However, not every payroll system is the best fit for your organization.

If you are a small church organization, economy will be important. You might have limited staff. In these cases, it might be optimal to outsource payroll to a service provider that can process payroll for you.

In other cases, you might opt to run your own payroll. One approach is to start with a basic payroll system and expand it into more functions (such as HR) as you grow. If you already are a large organization or a PEO that is serving multiple smaller churches or organizations, the best choice will likely be a fully functional payroll and HR system.

Regardless of the solution that you choose, it is advantageous to find a system that is user-friendly and easy to learn, and a vendor that offers excellent customer support. If you’re looking for individual product reviews, with even more analysis, check out our articles on Rippling and Paychex .