Church Payroll: Software, Services and Clergy Tax Rules

For a small church paying one pastor and three staff, published payroll software prices run from about $59 to $128 a month as of October 2026, depending on the vendor and plan. The software is the easy part. The harder part is that pastors are taxed differently from other employees, and a payroll setup built for an ordinary small business can get that wrong.

This guide compares published prices, shows the monthly math for a typical small church, and gives a checklist for clergy pay to review with your CPA. It is not tax advice.

TechSoup QuickBooks does not include payroll

Many churches run their books on QuickBooks Online Plus through TechSoup for an $80 annual admin fee. TechSoup's QuickBooks Online page states that add-ons such as Payroll are not available through it, so Intuit bills payroll separately at its regular rates. There are two more catches worth knowing before you switch:

• The donated subscription has to be a new account, and Intuit payroll data cannot be transferred between subscriptions. If you run QuickBooks Payroll on a commercial account today, plan the move for a clean break point, such as the start of a calendar year or quarter.
• Your accounting discount does not reduce payroll cost. A church on TechSoup QuickBooks still pays full price for payroll.

Our church accounting software pricing guide covers the accounting side, and the QuickBooks TechSoup migration guide covers the switch itself.

Published payroll prices (as of October 2026)

Provider	Plan	Base fee	Per person	Source
Square Payroll	Full-service payroll	$35/mo	$6/mo	Square pricing
Gusto	Simple	$49/mo	$6/mo	Gusto pricing*
QuickBooks	Workforce Payroll	$50/mo	$7/mo	Intuit Workforce Payroll
Gusto	Plus	$80/mo	$12/mo	Gusto pricing*
Gusto	Premium	$180/mo	$22/mo	Gusto pricing*

*Gusto's figures were confirmed on Gusto's own plan pages (Simple, Plus, Premium) on October 18, 2026. Gusto bills month to month with no contract.

Notes on the QuickBooks figures:

• Intuit's Workforce Payroll page shows a $25/month promotional base price for 3 months. Its footnote says the discount applies only to the base price, not to per-employee fees or state tax filing fees, and that you pay the then-current price after that.
• Intuit's payroll pricing page shows bundles of payroll and accounting, for example Workforce Payroll plus QuickBooks Essentials at $125/month plus $6.50 per employee. That per-employee rate differs from the $7 shown on the payroll-only page, and we could not read the footnotes that would explain it. Ask Intuit which rate applies to your account.
• Square also lists a contractor-only plan at $6 a month per person paid, with no base fee.

The Square and Intuit pages we read don't mention a nonprofit or church discount, and our database lists no Gusto nonprofit discount.

Worked example: 1 pastor and 3 staff

Assume a church pays 4 people each month: 1 pastor, 1 administrator, and 2 part-time staff. Using the published regular prices above:

Plan	Monthly math	Monthly	Annual
Square Payroll	$35 + (4 × $6) = $35 + $24	$59	$708
Gusto Simple	$49 + (4 × $6) = $49 + $24	$73	$876
QuickBooks Workforce Payroll	$50 + (4 × $7) = $50 + $28	$78	$936
Gusto Plus	$80 + (4 × $12) = $80 + $48	$128	$1,536

If the church keeps QuickBooks Online Plus through TechSoup and adds QuickBooks Workforce Payroll, the combined yearly cost is $80 + $936 = $1,016. Compare that with Intuit's commercial Plus list price of $140 a month ($1,680 a year) before payroll, which is the price a church pays if it never applied through TechSoup.

The difference between the cheapest and most expensive plan in this example is $1,536 − $708 = $828 a year. Before choosing on price, check two things: whether the plan covers every state where you have employees, and whether it can handle a minister's pay correctly, covered below.

If you want to see how payroll fits with the rest of your software spending, the free audit lists each tool you pay for and the nonprofit price available for it.

How clergy pay differs

IRS Publication 517 (the 2025 edition, for 2025 returns) is the main IRS source on clergy taxes. In plain terms, as of October 2026:

• Dual status. A minister can be an employee for income tax purposes while being treated as self-employed for Social Security and Medicare on ministerial earnings. Publication 517 says clergy receive a Form W-2 but do not have Social Security or Medicare taxes withheld, and they pay those taxes through Schedule SE.
• No required income tax withholding. Publication 517 says a minister's salary for ministerial services isn't subject to federal income tax withholding, but a minister can enter into a voluntary withholding agreement with the church.
• Housing allowance. The IRS FAQ on ministers' compensation says the allowance must be officially designated in advance of payment. The amount excluded from income is the smallest of the designated amount, the amount actually spent on housing, and the home's fair rental value, and it can't exceed reasonable pay for the minister's services.
• Still counted for self-employment tax. The same FAQ says the housing allowance is excludable for income tax but not for self-employment tax.
• Exemption option. Publication 517 describes Form 4361, which some ministers file to request exemption from self-employment tax on ministerial earnings.

These rules apply to earnings from ministerial services. Whether a particular person, or a particular part of their pay, falls under them is a legal and tax question. Your CPA should make that call, including for staff such as an administrator or worship leader.

Clergy payroll checklist (risk reduction, not tax advice)

Use this list to prepare for a conversation with a CPA who works with churches:

1. Written designation. Does your board or governing body adopt a written housing allowance designation before the payments it covers, with a definite amount?
2. Annual review. Is the designated amount reviewed each year against the pastor's expected housing costs?
3. Payroll settings. Is your payroll software set up so that no Social Security or Medicare tax is withheld from the pastor's ministerial wages, while it is withheld for non-ministerial staff? Ask each vendor directly whether and how it supports ministers. We have not verified clergy features for the providers above.
4. Housing allowance in payroll. Does your provider record the housing allowance separately from salary so it can be excluded from taxable wages where appropriate?
5. Income tax withholding. Does the pastor have a voluntary withholding agreement, or does the pastor make estimated payments instead?
6. Form 4361 status. Do you know whether your pastor has an approved exemption on file?
7. Switching providers. If you change payroll software, can you do it at the start of a quarter or year to avoid splitting filings?

When to use a service instead of software

Payroll software still needs someone to enter hours, approve each run, and keep the clergy settings right. Some churches hand the whole job to a bookkeeper or outside firm. NonProfitSaver offers its own finance operations service, which includes payroll processing and housing allowance administration alongside bookkeeping; it does not include tax advice. Whoever you hire, ask for a written scope that names who is responsible for clergy payroll setup.

For other ways churches cut software costs, see church software discounts and our guide to church eligibility for nonprofit discounts.