Integrate with Aplos

Aplos is a software solution for churches and nonprofits that lets you manage your books, donors, and members all in one place.

Services include:

Gusto connects to Aplos Accounting to automatically track your payroll and tax payments. We also support the W-2 requirements and unique church payroll needs for pastor housing allowances and tax exemptions. 

Learn more by visiting Aplos' help center.

Connect to Gusto from your Aplos account

  1. Navigate to the Accounting section of your Aplos account.
  2. Click Payroll.
  3. Click Log in to your Gusto account.
  4. Enter your Gusto login credentials.
  5. Click Authorize.
  6. Click Go To Setup to set up how the payroll details will map to your Aplos accounts.
  7. Select the Fund account and assign an expense or liability account for each category.
    • Click the + next to a category and adjust the percentages to split the entry between multiple accounts.
    • Your bank account election can be an expense or an asset account.
  8. Click Save.

You'll now see the active integration in the App directory section of your Gusto account.

Account mappings

Edit your global account mappings

  1. Navigate to the Payruns for Import page in Aplos.
  2. Click the gear icon in the top right hand corner.

Customize your account mappings by employee

  1. After you’ve clicked import for a payrun, uncheck the box in the Edit Mapping column.
  2. To override the global mapping setting(s) and customize to the employee, select a new account in the field you’d like to override and enter a percentage.
    • Fields not edited will apply the global settings when mapping accounts.
    • Employee’s custom mappings will be applied on future payroll imports until otherwise edited.
  3. Click Save.
    • The total accounts customized will appear in the Custom Mappings column.

Remove or reactivate a payrun

  1. Click Show History.
  2. Click Reactivate if you’d like to make a previously dismissed payroll available for import.
  3. Click Remove Payrun if you want to remove any existence of that previously imported payrun in Aplos.
    • The payrun will then become available to import or dismiss again.


Q: Does information sync over by employee?

A: Yes. Everything from payroll taxes, wages, and reimbursements can be mapped on an individual level. Click 'Account mappings' above to learn more.

Q: How do I set up a tax exemption?

A: There are two types of exemptions, employee or employer. Click here for steps to set up an exemption.

Q: How do I add a reimbursable housing allowance when processing payroll?

A: Follow the instructions in this article to add the housing allowance amount as a recurring reimbursement

Remember to make sure the allowance is an official housing allowance that's excluded from taxable gross wages. 

Learn more about housing allowances here.

Q: How do I handle the annual housing allowance so it is reported on Form W-2?

A: You can reimburse your pastors throughout the year, then at year end be sure to enter the yearly totals in Gusto when confirming your 2021 tax information.

Q: Does the sync work on regular, off-cycle, and bonus payrolls?

A: Yes.

Q: Will I be able to distinguish between a direct deposit or check payment to an employee in Aplos?

A: Yes. 

Q: Do you have any additional resources we can reference?

A: Check out this IRS resource with tax information, filing requirements, and exemption information for charities and other non-profits.