Integrate with QuickBooks Desktop

QuickBooks Desktop is a desktop accounting software for businesses who need industry-specific features and reporting. QuickBooks Desktop features include inventory tracking and job costing with the beauty of online collaboration and the speed of running QuickBooks Desktop on your local machine. 

With our QuickBooks Desktop integration, you can export an Intuit Interchange Format (IIF) file containing your payroll information and upload it into QuickBooks Desktop software. This is compatible with all versions of QuickBooks Desktop that support IIF imports, including Mac, Pro, Premier, and Enterprise versions. You can upload your chart of accounts directly from QuickBooks Desktop and use your customized accounts to create a journal entry. There are also options for additional levels of granularity within the entry based on earnings types and Gusto departments.

AI-powered mapping suggestions

This integration now includes an AI-powered feature that helps you choose the right accounts when setting up mappings for your chart of accounts. This is especially helpful if you’re not sure which account to pick for a payroll category.

Example: Say you’re setting up default accounts and don’t know what to choose. Gusto might suggest using Payroll Wages for Wages & Salaries, or Payroll Deductions Payable for Deductions.

How suggestions are generated

Gusto’s AI provides recommendations based on:

  • Industry standard accounting guidance from US-based CPA firms
  • Common account structures used by thousands of small and mid-sized businesses
  • Aggregated, anonymous patterns from other Gusto customers who use platforms like QuickBooks Online, Xero, and FreshBooks.

The AI model never stores or accesses your personal financial information. All suggestions are based on general patterns, not individual data.

Manage default and detailed mapping

Why default mappings matter

Over time, you may make changes to your Gusto account such as adding a custom deduction, creating a new earnings type, or setting up a new benefit. When this happens, new payroll line items are created in Gusto that need to be mapped to an account in QuickBooks Desktop. If these items are not mapped, they can cause sync issues. Setting up default mappings can help you with this.

What default mappings do

Default mappings let you pre-select the QuickBooks Desktop accounts that should be used for new payroll categories. This means that when you create a new line item, you will not have to manually map it to a QuickBooks Desktop account—Gusto will automatically apply your default mapping to it.

  • Example: If a new earnings type is created in Gusto, it will appear under "Wages & Salaries." If you’ve already chosen a default mapping for “Wages & Salaries,” the new line item will automatically map to the default QuickBooks Desktop account without interrupting the sync.

Setting up default mappings is optional. If you prefer to manually map new Gusto categories, simply leave the default mapping blank.

Set up default mappings

Follow these steps to set up or change default mappings:

  1. In your Gusto admin account, head to the App directory.
  2. Go to the Connected Integrations tab.
  3. Choose QuickBooks Desktop.
  4. Select the Default tab.
  5. For each section (Wages & Salaries, Employer Taxes, etc.) you’d like to map, select the QuickBooks Desktop account you want new categories to map to.
    • If you prefer to manually map new categories as they’re created, simply leave the default mapping blank.
  6. Repeat for all sections.
    • Your selections are saved automatically.

Edit default mappings

You can change default mappings at any time in the Default tab. Changes will only apply to new mappings going forward. 

Edit detailed mappings

If a new category has been given a default mapping you’d like to change, you can change it in the Detailed tab. Here's how:

  1. In your Gusto admin account, go to the App directory
  2. Go to the Connected Integrations tab.
  3. Choose QuickBooks Desktop.
  4. Select the Detailed tab.
  5. Find the category you’d like to change and select the QuickBooks Desktop account it should map to going forward. 
    • If you also want to change the default mapping for line items in that category going forward, go to the Default tab.

If you want these adjustments to reflect on past payrolls, you'll need to manually re-download the IIF file.

Consolidated mapping

To provide more granularity, you have the option to map your chart of accounts by employee, job, department, or Gusto Projects (available to companies using Gusto Project Tracking). If you use QuickBooks Classes, you can also assign a class to each of the selected grouping options.

This is optional.

Set up consolidated journal entries

Step 1: Choose your journal entry consolidation method

  1. Sign in to your Gusto admin account.
  2. Go to the App directory and select QuickBooks Desktop.
    • You can also find this under the Connected Integrations tab.
  3. Under Settings, go to the Manage tab.
  4. Next to "Journal entry consolidation," click Edit.
  5. Choose how you want to consolidate entries:
    • By employee
      • This can offer more detailed reporting. 
      • Ex: You can track each employee’s wages in separate accounts instead of one "Salaries and Wages" account.
    • By department:
      • This can help you track wages, taxes, and benefits separately. 
      • Ex: You can send Design wages to one account and Marketing wages to another, instead of combining everything into "Salaries and Wages." You can also map departments to QuickBooks Classes if needed.
      • Click here to see how you can enable departments.
    • By job:
    • By project:
      • Gusto Project Tracking must be enabled. We do not integrate with QuickBooks Projects.
      • You can track wages, taxes, and benefits by project. 
      • Ex: Instead of all wages going to “Salaries and Wages,” you can split wages into separate accounts for each Gusto Project. 
  6. Click Submit.

Step 2: Set up mapping overrides and Quickbooks Classes (optional)

Once you select a consolidation method, a new tab appears on the left. Ex: If you choose to consolidate by employee, the tab will be called Employee. If you choose to consolidate by department, the tab will be called Department.

You can override default mappings for individual employees, departments, jobs, or projects. Overriding a default mapping means assigning different accounts to payroll items at these levels. 

This is optional—if no overrides are applied, journal entries will still be categorized accordingly.

Here's how to set up an override:

  1. Find the new tab that corresponds to the consolidation method you chose.
    • Ex: If you chose to consolidate by employee, go to the Employee tab.
  2. Click Override.
  3. If your company uses QuickBooks Classes, you’ll first have the option to choose a tracking category.
  4. Just as you did on the Detailed tab, match each Gusto category to an account in QuickBooks.

Contractor payments

Consolidating journal entries by employee and department is compatible with contractors.

Consolidating by job and project is not compatible with contractors. This is because job titles and Gusto Projects are not currently supported for contractor profiles. If your company pays contractors and uses job or project consolidation, contractor payments will be synced based on the default company mappings.

Print checks from QuickBooks Desktop

If you pay employees by check, we recommend you print the checks from Gusto.

If you prefer to print checks from within QuickBooks Desktop, you can do this by editing the Journal Entry in QuickBooks Desktop. This prevents double reporting.

For any checks that will be printed from QuickBooks Desktop, we recommend updating the bank account line item on the Journal to a liability account or clearing account. When you create the check in QuickBooks Desktop, you should code the line item to the same liability or clearing account, which will offset the account balance.

Click here for steps to find and edit Journal Entries in QuickBooks Desktop.

FAQs

Choose a section below for frequently asked questions about this integration.

General

Q: Do you support QuickBooks Classes?

A: Yes. See the “Consolidated mapping” section above. 

Note: If you would like to map QuickBooks Desktop Classes to your Journal Entry consolidation options (employees, departments, jobs, or Gusto Projects), be sure to tick the "Classes" option when exporting your chart of accounts.

Q: The chart of accounts in Gusto does not look correct. What should I do?

A: Unlike online accounting integrations like QuickBooks Online, QuickBooks Desktop is an offline product and does not receive data through an automatic sync. 

If the chart of accounts is not correct, upload a fresh chart of accounts. For steps to upload a new IIF file, refer to the "Connect QuickBooks Desktop to Gusto" section of this article.

Note: Accounts Receivable and Accounts Payable account types are not supported at this time because these require a Contact to be used with the Account. Asset and Liability accounts are supported without a Contact.

Q: How do I handle checks?

A: We recommend printing checks from your Gusto account or handwriting them. You can then reconcile the journal entry from Gusto when your employees cash the checks. We do incorporate the amount of each check in our Journal entry.

Default mapping

Q: Why can’t I find the QuickBooks account I’m looking for in the drop-down?

A: The initial list in the drop-down menu shows recommended accounts based on the selected category. To choose a different account, simply type the name of the account into the search box.

If you still cannot find the account, upload a new chart of accounts. Refer to the "Connect QuickBooks Desktop to Gusto" section of this article.

Q: Do I need to select a default for each section?

A: No, you are not required to select a default for every section. If you prefer to manually map specific sections, you can simply leave those sections blank.

Q: What happens if I do not set up default mappings?

A: Default mappings are designed to automate mapping of new payroll categories that are added to your integration. If you choose not to enable default mappings, you will need to manually select the appropriate account for each new payroll category. 

You cannot download journal entries until all categories are mapped to an account in QuickBooks Desktop, which may disrupt your integration process.

Q: When are new mapping categories created?

A: New categories may be created in your integration under the following circumstances:

  • Adding a deduction
  • Creating a new earning type
  • Setting up a benefit for the first time
  • Establishing a new time-off policy
  • Relocating to new states, such as New York (NY) or Hawaii (HI)
  • Requesting payroll adjustments

Each of these actions can introduce new payroll categories that will require appropriate mapping to ensure your integration functions smoothly.

Q: If I set up or change default mappings, will that impact what I’ve already mapped on the Detailed tab?

A: No, this will only impact new categories that may be added to your integration going forward. If you would like to adjust your detailed mappings, you can do so manually in the Detailed tab.

Q: Can I change my default mapping selection later?

A: Yes, you can change your default mapping selections at any time. Please note that any changes will only affect future mappings. Your existing mappings will remain unchanged.

Detailed mapping

Q: If I update my mappings, can I re-sync a payroll to update the bill or journal entry?

A: Yes. To re-sync a payroll:

  1. After updating your mappings, go to the Pay tab in Gusto.
  2. Choose Pay History.
  3. Download a new IIF file.

Q: How do I break out individual employee payroll items?

A: You can change the journal consolidation method to “by employee.” To do this,

  1. Go to the Settings tab and choose Manage.
  2. Next to "Journal entry consolidation, click edit.
  3. Select Employee.

Q: Why can’t I find the QuickBooks account I’m looking for in the drop-down?

A: The initial list in the drop-down menu shows recommended accounts based on the selected category. To choose a different account, simply type the name of the account into the search box.

If you still cannot find the account, upload a new chart of accounts. See the "Connect QuickBooks Desktop to Gusto" section of this article for steps to upload a new IIF file.

Q: What if I will not be using one of the payroll items listed?

A: The item will still need to be mapped to an account. If the payroll item is not applicable, nothing will sync related to the account that is selected within your entry. Only payroll items that apply to a processed payroll will populate within the synced entry.

Q: Can I include employee benefit deductions on the Journal Entry?

A: Employee deductions are included in the gross wages amounts that are reported on the Journal Entry. These are not tracked separately because they're not an additional expense to the company on top of what's already reported for wages.

Employee deduction amounts are included in the Benefit Liability along with the Employer Contributions. Click here to learn more.

Q: Can unique reimbursements be broken out through separate mappings?

A: No, all reimbursements will be pushed over as a lump sum (e.g. Cell Phone Reimbursement + Gym Reimbursement + Office Supplies Reimbursement, etc.).

Consolidated mapping

Q: Can I use more than one tracking category or journal consolidation method? For example, can I consolidate my journal entries by employee and by job?

A: No, not at this time. You must choose to consolidate by one method (by employee, department, job, or project). Next, you may select one class for each employee, department, job, or project. 

Q: Can I change the way I consolidate my mappings?

A: Yes, you can change your consolidation preferences at any time. Under Settings, go to the Manage tab. Keep in mind that any changes will result in the deletion of previous consolidated account mapping overrides. Your company’s Detailed mappings will be retained. 

Q: Do I need to set up overrides for consolidated mappings? 

A: Setting up overrides for consolidated mappings is entirely optional. While it's not required, it does provide you the opportunity to customize the mappings layout for each unique grouping you've established.

Q: Is it necessary to establish a QuickBooks Class for each consolidated grouping? 

A: No, it's not mandatory. This is optional based on your specific needs.

Q: Is it possible to assign multiple QuickBooks Classes to a single consolidated grouping? 

A: Currently, our system allows only one QuickBooks class to be assigned per consolidated grouping.

Q: Do you offer an integration with QuickBooks Projects? 

A: We do not currently offer direct integration with QuickBooks Projects. If you opt to consolidate your mappings by project, we will segment each entry according to the projects you've configured in your Gusto Project Tracker. However, please note that this information will not be directly pushed to QuickBooks Projects.

Syncing

Q: Why is there an error when I try to upload the journal entries to QuickBooks Desktop?

A: Upload errors typically occur when there is a mismatch between the accounts listed in Gusto and the accounts in QuickBooks Desktop. 

Here's how to fix an upload error:

  • Upload a fresh chart of accounts to Gusto.
  • Download a new IIF file for the payroll or contractor payment.
  • If the error persists, review the IIF error file generated by QuickBooks Desktop.
  • After the issues are resolved, upload the payroll’s IIF file to your QuickBooks account again. 

Q: If I update my mappings, can I re-sync a payroll to update the bill or journal entry?

A: Yes. To re-sync a payroll:

  1. After updating your mappings, go to the Pay tab in Gusto.
  2. Choose Pay History.
  3. Download a new IIF file.

Q: How do employee taxes and employee benefit contributions sync to QuickBooks Desktop?

A: They’re always included in Gross Wages & Salaries. 

Q: Do you break out individual taxes?

A: Gusto handles all of your tax payments automatically. Because of this, you do not need to track tax liabilities. When we sync entries, we record employer taxes as expenses. 

You can select for employer taxes to be broken by each individual tax or lump them together. You’ll find this option under Settings under the Manage tab. 

At this time, we only support one account mapping which will be used across all employer taxes. 

Employee taxes are not broken out individually for mapping or in journal entries, as these values are included in Gross Wages. 

Q: How do contractor payments sync over?

A: You have two options for syncing contractor payments. See the "Connect QuickBooks Desktop to Gusto" section of this article for more information.

Q: Can I sync international contractor payments to QuickBooks Desktop?

A: Yes, both US-based and non-US based contractor payments can be synced. To do so, go to the Pay section in Gusto and choose Pay history. Go to the Contractor payment history tab and select a payment to sync.

Q: Can I sync international employee payrolls to QuickBooks Desktop?

A: Not at this time.

Q: Can I sync Gusto or NEXT insurance invoices to QuickBooks Desktop?

A: Not at this time.

Disconnect the integration

If you need to troubleshoot the connection or if you no longer want data to sync between Gusto and QuickBooks Desktop, follow the steps below to disconnect the integration. You can reconnect at any time.

  1. Sign in to your Gusto admin account.
  2. Go to the App directory.
  3. Search for and select QuickBooks Desktop.
  4. Go to the About tab.
  5. Click Disconnect app.