Answers to Common Questions

Whether you're new to outsourcing payroll or already have experience with it,
you'll find answers to frequently asked questions about MinistryWorks here.

  • What happens if I submit my payroll electronically with a mistake?

    When a mistake is discovered on a payroll that was submitted electronically, the MinistryWorks staff will work with your ministry to correct the mistake as efficiently as possible. Each mistake is separately evaluated, and the best solution is chosen to satisfy the ministry and the employee.

  • How do I handle holiday payroll and back up processing?

    When your ministry becomes a client of MinistryWorks, a payroll processing calendar is established for you based upon your pay dates. At that time, you will indicate whether your ministry desires to move your pay day back or forward when the pay day falls on a holiday. The calendar is adjusted based upon this decision.

  • What kind of software do you use?

    MinistryWorks sets all our customers up on our easy-to-use payroll processing software. The system processes payroll efficiently and produces comprehensive reports. From simple to complex payroll needs, this dynamic system is capable of handling multiple earning and deduction types. It provides accurate calculating, reporting, and payment of your ministry’s tax liabilities.

  • Is your system secure?

    Data security is a primary concern facing nearly all industries today. At MinistryWorks, we’re committed to protecting your ministry’s confidential payroll data. Here’s a list of just some of the ways we protect your ministry’s sensitive payroll information.

    • All information shared electronically is encrypted using industry standard SSL technology.
    • Only authorized MinistryWorks professionals have access to the computer system used to process your ministry’s payroll.
    • All paper documents are stored in locked filing cabinets in a secured area within the MinistryWorks department.

    MinistryWorks is committed to implementing and maintaining security procedures that protect your ministry.

  • How do we get started?

    If you’re ready to get started with MinistryWorks, call us at 866.215.5540 or submit the online form. We look forward to working with you. Contact us.

  • What is the onboarding process like?

    We make every effort to keep your transition to MinistryWorks simple. There are basically three steps involved. First, we work with you to complete your payroll needs analysis and have you sign a few forms, then we work with you to gather the necessary reports from your current system. Finally, we run several test payrolls to ensure all calculations are correct.

Payroll Processing
  • How are special payroll deductions handled?

    Special payroll deductions such as health insurance premiums, membership dues, charitable contributions, etc. are calculated and withheld from the employee’s payroll during each pay period. These deductions are clearly reflected on your ministry’s payroll check register so you can pay your ministry’s deduction liabilities directly to the appropriate vendor.

  • How do we retrieve our payroll reports?

    There are a couple of options for receiving payroll reports from MinistryWorks. Electronic reports are available for download from the website within moments after your payroll processing is complete. After each payroll is processed, you will receive an email alert that the reports are available for download. The report files are in PDF format and can be viewed, downloaded, and printed. 

  • How do our employees receive their paystubs?

    If your ministry chooses the direct deposit option for your employee’s pay checks, an ACH voucher is created for each employee and is included in the report package that is generated with each payroll. Employees can receive their paystub via email, or by logging into ESS (employee self serve). Your payroll administrator can also print a copy of each paystub for delivery to the employees on pay day. The payroll funds will be automatically deposited into the employee’s bank account.

    Direct deposit is a safe and efficient method for paying your employees. Funds are automatically deposited into the employee’s bank account, eliminating the expense of producing and reconciling checks.

    If your ministry chooses the paper check option for your employees’ pay checks, the checks will be delivered via courier. Your payroll administrator can deliver the checks to the employees on pay day.

  • What happens if we have a problem with the IRS?

    When your ministry becomes a client of MinistryWorks, you will sign a limited power of attorney document. This document allows MinistryWorks to make payroll tax deposits, file and sign payroll tax returns, and receive information related to these payroll tax returns from the IRS or applicable state taxing authority. As the employer, you remain responsible for any tax that is legally owed by your ministry; however, MinistryWorks will work to alleviate any issues that stem from our error in processing. This includes communicating with the IRS regarding the issue and paying any fine or penalty incurred as a result of our error.

  • How are our taxes paid?

    MinistryWorks withholds federal, state, and local tax dollars with every payroll processed for your ministry. These funds are held in MinistryWorks’ bank account until the taxes are due to be paid. MinistryWorks transfers the federal tax dollars to the IRS and the state/local tax dollars to the appropriate state taxing authority in accordance with your ministry’s current filing requirements. We generate the quarterly and annual federal and state tax forms, provide you with a copy, and file them with the IRS and other appropriate tax agencies. The W2 documents are prepared and sent to your ministry for review and distribution at each year end. As required by law, copies of the W2 documents are also provided directly to the Social Security Administration.

Customer Service
Customer Service
Customer Service


Your payroll needs are unique, so you probably have questions. We’re ready to assist you.

You could claim up to $33,000/employee with the
Employee Retention Credit.

Select your organization type
to learn more.

I'm a ministry I'm a school