Home Church Management Do Nonprofits or Churches Need to Complete 1099s?

Do Nonprofits or Churches Need to Complete 1099s?

by Aplos Success Team

Any organization that meets the filing requirements is required to complete 1099s, regardless of tax-exempt status. Form 1099 is a required IRS report that documents the amount of certain types of income paid to an individual. Most commonly, these are sent to people who provided a paid service for your organization, such as a contractor or vendor. Generally, 1099s are required if the amount paid is at least $600 in a year, although there are some exceptions for other forms of income.

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If you aren’t sure whether you should issue a 1099, we recommend consulting with a CPA or trusted professional for tax or accounting advice.

When Are 1099s Due?

1099s need to be mailed by January 31 each year. You can purchase the necessary forms at office supply stores, and then use Aplos Accounting to make it easy to print your report. These are then mailed to the contractor or vendor.

Your nonprofit organization will also need to file a Form 1096 with the government, which is basically a list of all the 1099s you sent out. Typically, when you buy a pack of 1099s from the store, it will come with the 1096 and instructions for filing it. The filing deadline for 1096 forms is also January 31.

Which 1099 Form Do You Need to File?

There are many different types of 1099 forms. These variants are based on the income source, but here are some of the more common ones:

Common 1099 Forms


The IRS made significant changes for 1099 reporting for the 2020 tax year. Beginning in January, 2021, the 1099-NEC form will now be used for reporting nonemployee compensation (NEC) payments. Previously, this was noted in a box on the 1099-MISC form. 

Nonemployee compensation is one of the most common types of payments made by nonprofits and churches that will need to be reported on a 1099. Generally, you must issue a 1099-NEC if all the following conditions are met:

  • You made the payment to someone who is not your employee.
  • You made the payment for services in the course of your trade or business (including government agencies and nonprofit organizations).
  • You made the payment to an individual, partnership, estate, or, in some cases, a corporation.
  • You made payments to the payee of at least $600 during the year.

Review the full IRS guidelines for 1099-NEC instructions on qualified payments or consult your accountant for advice.


Prior to the 2020 tax year, the 1099-MISC was frequently used by nonprofits and churches. However, since the new 1099-NEC form accounts for the nonemployee compensation, there will be some organizations that won’t use the 1099-MISC form as much going forward. Learn more about the changes for the 2020 tax year on the IRS website.

Organizations will need to fill out a form 1099-MISC if they paid at least $10 in royalties or broker payments in lieu of dividends or tax-exempt interest, or if $600 or more per year is paid in the following circumstances:

  • Rents
  • Prizes and awards
  • Other types of payments not covered by another information reporting document
  • Generally, the cash paid from a notional principal contract to an individual, partnership, or estate
  • Any fishing boat proceeds
  • Medical and healthcare payments
  • Crop insurance proceeds
  • Payments to an attorney
  • Section 409A deferrals
  • Nonqualified deferred compensation

Still not sure which 1099 form you should issue? We recommend consulting with a CPA or trusted professional for tax or accounting advice.

 Learn How To Become A 1099 Expert!

Get ready to create and generate your own 1099s within Aplos. In this webinar, Alex Acree, Head of Customer Success at Aplos, will:

  • Discuss which vendors are eligible for 1099s and the recent changes to the form by the IRS
  • Share tips and tools for how to use Aplos to track your vendors
  • Review the process for how to generate this IRS-required document in Aplos

Fill out the form below to quickly improve your 1099 skills!

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Robert St. Cyr December 16, 2019 - 4:05 pm

I understand Aplos doesn’t print 1099s for amounts less than $600. What if I want to provide my contractors a 1099 anyway so I have to do it outside of Aplos? Also what if I want to do a 1096 and include those amounts?

Clay Harmon December 18, 2019 - 11:44 am

Hi Robert,

That is correct. Our 1099 and 1096 are only over $600, as that is the IRS requirement. Anything below that amount you’ll have to generate outside of Aplos.

Nadine Gonzalez January 21, 2022 - 9:51 am


I work a non profit organization which helps house the homeless. The rent we pay the the landlords for the otherwise homeless.
Do we issue a 1099-NEC to the lessors of the rental property who issue a W-9 using their personal social?

Aplos Success Team January 21, 2022 - 10:33 am

Great question, Nadine. While we wish we could help, we can’t provide accounting advice for your specific situation. We recommend reaching out to a local accountant who provides consulting and can review those agreements to see if they would qualify.

Robert January 25, 2022 - 8:45 am

Hello Nadine,

Did you ever get any guidance or answer to your question here?

Kathy Fissel January 31, 2022 - 10:03 am

The beginning of the guide states that payment in Excess of $600;
later on it states payments of at least $600.

Is the ruling $600 and over
or Over $600?

Aplos Success Team January 31, 2022 - 11:02 am

Hi Kathy,
Thanks for catching that. The instructions say “At least $600.” https://www.irs.gov/instructions/i1099msc

Jay February 19, 2022 - 3:49 pm

We are a non-profit which helps with peoples’ rent and utilities. If our assistance to an individual exceeds $600 is this considered income to them and therefore we need to provide the individual with a 1099.

Aplos Success Team February 22, 2022 - 3:10 pm

Hi Jay,

We aren’t able to provide tax or accounting advice on your specific organization’s situation. We recommend talking to an accountant in your area who can review your particular circumstances.


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