What Taxes Can Churches Withhold For Pastors?

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Thanks to the Tax Cuts & Jobs Act, people are paying a whole lot more attention to their tax withholdings this year. Employers had a hard time calculating withholdings with all the changes in the law and the result was far fewer people getting big tax returns (which I think is actually a good thing!) and more people owing. (Don’t get mad at the employers, though, no one really knew how it would all play out.)

So, with this renewed interest in tax withholding, I thought it would be a good time to go over how it all works for pastors. Because this is yet another area where it’s different for pastors than for everyone else. While some church employees do have to pay their taxes differently, the information in this article is only for pastors and does not apply to non-ministerial church workers.

Mandatory Withholdings

If you work a secular job, your employer withholds money from every one of your paychecks to cover federal income taxes, Medicare taxes, and Social Security taxes. They do it regardless of how you feel; you have no say in the matter. Because it’s the law.

Well, this is an area where pastors are truly above the law. Or at least they are an exception to the law. There is no mandatory withholding for pastors on those taxes. That means that your church is allowed to pay you all of the money you’ve earned, without sending some to the government first.

FICA/SECA (Payroll) Taxes

In fact, not only do they not have to withhold taxes, but churches aren’t allowed to withhold Social Security and Medicare taxes (also called FICA or payroll taxes). This is because pastors always have to pay those taxes under the SECA program (as opposed to FICA) as if they were self-employed. If a church withholds FICA taxes for a pastor, they are breaking the law and will mess up his or her records with the Social Security Administration. Neither of those are good things.

Let me say it again because there seems to be a lot of confusion about this. Ministers always pay under SECA, not FICA. You don’t have a choice in the matter, it’s the law.

Also, you don’t get to decide whether or not you want to be treated as a minister. The work you do and your ordination/licensure determine whether or not you are a minister. It is not your decision. You can’t just have your church treat you like a regular employee. It doesn’t work that way.

Federal Income Taxes  

The IRS is more flexible with income taxes. While pastors aren’t required to have income taxes withheld, you are allowed to. Why would you want your church to withhold taxes if it isn’t required? Because you have to pay the taxes yourself if you don’t.

Like the rest of us, you pastors have to pay federal income tax. And like the rest of us, if you don’t have an employer withholding those taxes on a regular basis then you have to pay quarterly estimated taxes four times a year. Either way, the government is getting your money. A lot of pastors simply find it easier to have their church handle it rather than doing it on their own.

Withholding Extra

While your church can’t withhold payroll taxes, it is common practice to have them withhold extra income taxes to cover the amount that you will owe in self-employment taxes. When you file your taxes at the end of the year, everything you owe gets lumped into one tax bill regardless of whether it is for income tax, self-employment taxes, or something else. So, if you owe $5,000 in self-employment taxes and your church withheld an extra $5,000 in federal income taxes, then it all evens out in the end and you don’t end up with a big bill on April 15.

To do this, you first need to estimate how much you will owe in taxes. And don’t forget about the housing allowance when you make your calculations. I found a great online calculator for estimating pastors’ taxes here.

The calculator will show you how much you would owe in federal, Social Security, Medicare, and state taxes each paycheck. It also gives a breakdown of how much to pay each quarter if you pay the taxes on your own. You can use the same information to adjust your withholdings with your church. Then they will withhold enough to cover your entire tax bill and you don’t have to make quarterly estimated payments.


If you’re a pastor, it’s important to understand the nuances of your tax situation, even if you find it incredibly boring. Get over it and be proactive. Taking a little bit of time to prepare at the beginning of the year can save you a huge headache and a big hit to your bank account come tax time. You’ll be glad you did.

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20 Responses
  • Kim
    October 22, 2019

    Does a Pastor have to file a 1099 or a W2?

    • Amy
      October 29, 2019

      Whether a pastor has a 1099 or a W-2 will depend on whether he or she is considered an employee or independent contractor by the church. An employee’s wages are reported on a W-2 and an independent contractor’s payments are recorded on a 1099. I’ve seen pastors do it both ways.

  • joseph Dutton
    January 20, 2020

    Amy, As a Board member of a not for profit Ministry registered in the state of KY,(we do not have a 501c3 at this point) we have a church expression(that we serve as Elders of also) under our Ministry. The pastors receive compensation that is designated as 100% housing allowance. They also work secular full time jobs. Do we need to issue them a 1099 for last years compensation? Also, is there a way to help them offset the SECA they will owe due to the housing allowance?

    • Amy
      January 21, 2020

      Joseph,
      If 100% of their income was designated as a housing allowance, you do not need to issue 1099s. However, you do need to inform them of the amount you paid them as a housing allowance, though that could be done in a simple letter. You also do not need to report it to the IRS. The pastors will report it on Schedule SE when they file their taxes. The only way to help them with their SECA taxes would be to give them money, but that would be taxable compensation and subject to income taxes and SECA.

  • Gordon
    April 2, 2021

    Can a church withhold a portion of a Pastor’s SECA taxes from his salary? And is it legal for a church itself to pay the Pastor’s SECA taxes as a fringe benefit to the Pastor? Can you site the IRS publication(s) that rule on these matters? What IRS form is used to submit same to the IRS, and how often must it be submitted in a year? Thank you very much.

  • Gordon
    April 2, 2021

    Can a church withhold a portion of SECA taxes from a Pastor’s salary? And is it legal for a church to pay any part of a Pastor’s SECA taxes as a fringe benefit to the Pastor. What IRS forms are required for submission for either of these? What IRS documents support your answers? Thank you very much.

    • Amy
      April 2, 2021

      Gordon,
      When a pastor files Form 1040, both the federal income taxes and SECA taxes are lumped together into a final tax bill. Any withholdings are subtracted and the remaining balance is tax due while any excess withholding is returned as a tax refund. Churches cannot withhold taxes and call them SECA taxes, but they can withhold income taxes. Pastors can request that their church withhold enough in income taxes to cover both their income tax and SECA tax liabilities.

      A church can pay a pastor a benefit to help cover the cost of SECA taxes, but that benefit would be considered taxable income to the pastor. It would be lumped together with the pastor’s other taxable income on the W-2 regardless of the church’s intent for the money. As such, the church would not need to file any special forms.

      This is covered in IRS Publication 517 and the Journal of Accountancy explains it well here: https://www.journalofaccountancy.com/issues/2006/may/taxreportingforhousesofworship.html#:~:text=The%20amounts%20withheld%2C%20along%20with,the%20IRS%20on%20form%20941.&text=This%20amount%20also%20is%20reported,form%201096%20by%20March%201.

      • Gordon
        April 2, 2021

        Amy, Thank you for your prompt response. Please help me understand this part…In your 2nd line you state ” Any withholdings are subtracted…” but at the end you say “As such, the church would not need to file any special forms.” My question is how does the IRS know there are any withholdings if the church doesn’t report & submit it? Many thanks.

        • Amy
          April 5, 2021

          Employers who withhold taxes use Form 941 to report and submit them to the IRS quarterly. I meant that the church wouldn’t need to submit any additional forms if they were already doing that. I’m sorry for the confusion.

  • Dennis Campbell
    April 10, 2021

    Amy,
    I became treasurer of Westminster PCA in Clinton, SC this past year. I am in a squeeze for time right now as we have a new senior pastor to begin May 1 coming from an ARP church in Fla. and I have never set up a pastor’s payroll in our ACS Technology System. He has requested me to withhold Federal and State taxes from his paychecks. Our ACS system will calculate these amounts and withhold them based on his salary amount I put in. Since he is subject to SECA and not FICA taxes, I do not know what to do next and how to inform him on what I am going to do about that situation. I had no idea that I could not withhold FICA taxes on him until I just read about it in one of your articles. What do I need to do next?
    His financial package in addition to his salary includes housing allowance, insurance, retirement, and an expense a/c for church-related expenses. We have an Accountable Reimbursement Plan .Is there anything he or we can do to avoid SECA payments or help reduce them. To whom and how are they paid? Could you help me with this matter as soon as possible? I can supply you with $ amounts of each part of his package if you need them.

    • Amy
      April 12, 2021

      Dennis, there isn’t really anything you can do to avoid or reduce SECA. If you give the pastor extra money to help cover the cost, it is considered taxable income to him. This article explains how the taxes are actually paid: https://pastorswallet.com/how-pastors-pay-federal-taxes/ As for setting up payroll, that is beyond my expertise but I would recommend consulting with ascendbm.com or checking out freechurchaccounting.com.

  • Mary Bryan
    March 30, 2022

    Good Morning! We gave our Pastor a 1099 now he is saying we need to remove the amount we paid him and put a different amount. I dont want to do anything illegal can you help?

    • Amy
      April 8, 2022

      It depends on why he wants a different amount. If you included his housing allowance on the 1099 and he’s asking you to remove it, that’s correct. The amount on the 1099 should be the taxable income that you paid him.

  • Jon McDivitt
    August 10, 2022

    Good afternoon,
    One of our ministers was offered a salary package that he agreed to, prior to beginning his position at the church.
    This package was understood by the minister and Board of Trustees to have to be used for all areas, salary, housing, seca.
    Later, this minister complained privately and told our Finance Chairman that he had always received at least half of his SECA from the church as part of his package. The chairman alone, made the decision to give him extra money over and above his salary package. This was later discovered to the disappointment of other ministers and Board members. This benefit was not offered to all ministers, and was kept private.
    Is that ok, or should they offer the same benefit to all ministers working here.
    How should this be handled moving forward?

  • XiaoSou
    August 31, 2022

    Good morning, our church in Georgia will have a pastor and I believe we don’t need to withheld federal FICA or Futa, but what about state income tax? Our church is in process of getting 501(c3) status. Thanks

  • Nate
    January 19, 2023

    Hi Amy,
    Your link for the online calculator for pastor’s taxes is bad. https://www.startchurch.com/app/withholdings-calculator
    Thanks!

    • Forrest
      March 6, 2023

      Would love to also see that correct link

  • Bokman Han
    February 23, 2024

    Hi! Thanks for your blogs.
    Could you explain how the social security benefit messed up when the church withhold pastor’s social security tax?

    Quotes:
    “If a church withholds FICA taxes for a pastor, they are breaking the law and will mess up his or her records with the Social Security Administration.”

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