Introduction to QuickBooks Online Integration
The QuickBooks Online integration connects Factor to your QBO account to automate invoice syncing, expense importing, and payment tracking. All syncing happens in real time via webhooks — there are no manual export or sync steps required during day-to-day use.
What Syncs and How
Invoices (Factor → QBO)
When you finalize an invoice in Factor, it automatically creates a corresponding invoice in QBO in real time. Line items, amounts, client information, and payment terms all transfer based on your mapping configuration. The QBO invoice exists for accounting purposes - it is not sent to the client from QBO.
Expenses (QBO → Factor)
When a bill or expense is entered in QBO, Factor automatically detects the change and brings it in as an expense on the correct project. Checks do not import, so enter these transactions as a bill or an expense. Factor uses two pieces of information to match each line item to a project and an expense type:
The sub-customer on the QBO line item - must be linked to a Factor project
The product/service on the QBO line item - must be linked to a Factor expense type (see Step 3). Firms that do not use Two-Way Expense Sync can also link a chart of accounts item to an expense type (see Step 4).
Once matched, the expense appears on the project in Factor. If expense budgets for that expense type are set up on the project, the expense will automatically associate with the correct budget line and be available when preparing invoices.
If your firm has Two-Way Expense Sync enabled, expenses can also flow the other direction, from Factor to QuickBooks — see Two-Way Expense Sync for details. This is an optional feature set up with a Factor product specialist.
Payments (QBO → Factor)
When a payment is recorded against a Factor-originated invoice in QBO, it syncs to Factor and updates the invoice status automatically.
Voided Invoices
If an invoice is voided in either system, the void is reflected on both sides and cascades to related payment records.
Day-to-Day Usage
Once the integration is set up, no manual steps are required:
Finalize invoices in Factor - they appear in QBO automatically.
Enter bills or expenses in QBO against linked sub-customers and mapped products/services or expense accounts - they appear in Factor automatically.
Record payments in QBO against Factor invoices - the invoice status in Factor updates automatically.
Requirements
A QuickBooks Online account
Office Manager or Firm Owner permissions in Factor for initial setup
Setting Up QuickBooks Online Integration
Setting up the QBO integration involves connecting your QBO account to Factor, mapping Factor list items to their QBO counterparts, and linking your projects to QBO customers and jobs. Complete these steps in order.
Step 1: Connect Factor to QBO
Go to SETTINGS and click Integrations on the blue bar.
Click Connect to QBO.
Enter your QBO credentials and click Authorize.
You will be returned to Factor and the connection will be established.
Once connected, the following options appear:
Start Sync - No need to click this. It should only be used by your Factor product specialist.
Disconnect - Never click this without speaking to your product specialist first. Clicking it wipes all Factor QBO configurations and requires a call with a product specialist to reconfigure.
How should Factor create job names for jobs that don't exist in QuickBooks Online? - Controls whether the project number appears before or after the project name when Factor creates sub-customers in QBO.
Do you want to use invoice numbers generated by QuickBooks? - Determines whether QBO or Factor generates invoice numbers. The recommended setting is No (let Factor generate them).
Step 2: Map Service Types to QBO Products/Services
Each Factor service type must be linked to a QBO product/service so that invoice line items route to the correct income account in QBO. Most firms need three QBO products/services:
Factor - Firm Services - Income account for revenue from work your team performs
Factor - Subconsultant Revenue - Income account for subconsultant-related billing
Factor - Reimbursables Revenue - Income account for billable general expenses
To link service types:
Go to SETTINGS and click Lists on the blue bar.
Navigate to Service Types.
For each service type, select the appropriate QBO product/service in the QuickBooks Product/Services column.
Click the blue checkmark to save. Repeat for each service type.
Step 3: Map Expense Types to QBO Products/Services
Expense types also need to be linked to QBO products/services. In most cases, all subconsultant expense types map to the same product/service, and all general expenses map to the same product/service.
Go to SETTINGS and click Lists on the blue bar.
Navigate to Expense Types.
For each expense type, select the appropriate QBO product/service in the QuickBooks Product/Services column.
Click the blue checkmark to save. Repeat for each expense type.
Make sure all service types and expense types are linked to QBO products/services before linking your projects.
The product/service linked to an expense type is also used on the QuickBooks invoice line when that expense is billed to the client, so it needs an income account in QuickBooks. Firms that use Two-Way Expense Sync also need an expense account on the product/service, because pushed expenses are sent to QuickBooks as bills. See Two-Way Expense Sync for how to set up the product/service.
Step 4: Configure Expense Account Mappings for QBO Bills
This step applies to firms that do not use Two-Way Expense Sync. When Two-Way Expense Sync is enabled, the QuickBooks Expense Links list can be viewed but not changed, and new expenses import from QuickBooks only when the line item uses a product/service that is linked to an expense type (Step 3).
For bills entered in QBO to flow into Factor as expenses, you need to map QBO chart of accounts items to Factor expense types in the QuickBooks Expense Links area.
Important rules:
Mappings must be 1-to-1 - a QBO account cannot be mapped to more than one Factor expense type.
If your firm uses multiple subconsultant types, you need separate sub-accounts in QBO (e.g., 5010 Civil Engineering, 5020 Structural Engineering), each mapped to the corresponding Factor expense type.
Step 5: Link Projects to QBO
Projects are linked to QBO from the Billing Information section on the project's Overview tab. Click Link to QuickBooks to open the linking screen. There are three scenarios:
Customer and sub-customer already exist in QBO - Select both from the dropdowns and click Done.
Customer exists but sub-customer does not - Select the customer, then select Add as new sub-customer in the sub-customer dropdown. Click Done to create the sub-customer.
Neither exists in QBO - Select Add as new Customer and Add as new sub-customer. Click Done to create both.
Link new Factor projects to QBO as soon as they are created.
A project links to a sub-customer of its client's QuickBooks customer, so the sub-customer list shows only the sub-customers of the customer you select. Every project on a client shares the client's customer link. When other active projects on the client are already linked, Factor does not allow a different customer to be chosen for one of them. To use a different customer for just one project, link that project to a different or new client.
Unlinking a Project
On the project's Overview tab, in the Billing Information section, click Unlink next to Link to QuickBooks and confirm. Factor removes the project's link to its QuickBooks sub-customer. Nothing is changed or deleted in QuickBooks, and the client's customer link stays in place. You can also unlink from SETTINGS > Integrations > Mappings by clicking Unlink in the project's row.
To change a project to a different sub-customer, click Link and select the new sub-customer. Unlinking requires the Modify project overviews permission.
A project can be unlinked only while none of its invoices or expenses have been synced with QuickBooks. If any have, Factor shows a message and the link stays in place.
Don't Link to QuickBooks
In a project's Billing Information, check Don't Link to QuickBooks and save. The box can be checked only while the project is unlinked, so unlink the project first if needed. While it is checked:
The Link button is hidden for the project.
Finalizing its invoices does not prompt you to link, and its invoices and expenses are not sent to QuickBooks.
On SETTINGS > Integrations > Mappings the project shows Will Not Link and can be found with the Flagged filter.
On the Imported Projects page, the project shows Never Link in the Linked to QuickBooks column.
Uncheck the box at any time to link the project again.
Permissions
Configuring the QBO integration requires Office Manager or Firm Owner permissions in Factor.
Troubleshooting QuickBooks Online Integration
Connection Issues
The QBO integration is configured under SETTINGS > Integrations. If the connection has been lost, reconnect by clicking Connect to QBO and re-authorizing with your QBO credentials.
Warning: The Disconnect button wipes all Factor QBO configurations and requires a call with a product specialist to reconfigure. Never click it without speaking to your product specialist first. The Start Sync button should only be used by your Factor product specialist.
Invoices Not Appearing in QBO
If invoices are not syncing to QBO:
Ensure the invoice has been finalized in Factor - draft invoices do not sync.
Verify the project is linked to a QBO customer/sub-customer via the Billing Information section on the project's Overview tab.
Check that Don't Link to QuickBooks is not checked in the project's Billing Information. Invoices for those projects are not sent to QBO.
Check that all service types and expense types are mapped to valid QBO products/services under SETTINGS > Lists.
Confirm the integration connection is active under SETTINGS > Integrations.
Invoice Number Conflicts
If you are seeing duplicate or conflicting invoice numbers, check the setting under SETTINGS > Integrations: "Do you want to use invoice numbers generated by QuickBooks?" The recommended setting is No.
Expenses Not Importing from QBO
If expenses entered in QBO are not appearing in Factor:
Verify the transaction was entered in QBO as a bill or an expense. Checks do not import.
Verify the sub-customer on the QBO line item is linked to a Factor project.
Verify the product/service on the QBO line item is linked to a Factor expense type. Firms that do not use Two-Way Expense Sync can instead verify the chart of accounts item is linked to an expense type in the QuickBooks Expense Links area.
Remember: mappings must be 1-to-1 - a QBO account cannot be mapped to more than one Factor expense type.
Check BILLING > Synced Transactions. Transactions Factor has not imported yet appear there as Unmapped Project, Unmapped Expense Type, or Unmapped Tax Rate.
If the expense is not associating with the correct budget line, verify that an expense budget for that expense type is set up on the project.
Orphaned Expenses
If a bill was associated with a project in Factor and then deleted in QBO, the expense in Factor will display a yellow broken chain icon. This means the expense still exists in Factor but its QBO source record has been removed.
Bill Entry Tips
If a vendor's bill covers multiple projects, enter separate line items for each project.
If a bill applies to different phases, enter separate line items with the phase name in the description.
If part of a bill is fixed fee work and part is for reimbursables, enter them as separate line items since they may be billed differently to the client.
Bill images attached in QBO are also viewable in Factor.
Changes to a bill in QBO are reflected in Factor in real time.
Existing QBO Customer Hierarchy Issues
If your firm was using QBO before Factor, you may encounter issues linking projects due to how customers were previously configured:
No hierarchy - If your firm never used customer/sub-customer relationships and invoiced at the customer level, you may need to manually restructure in QBO first: create a customer for the client, move existing QBO customer records to be sub-customers under it, then link in Factor.
QBO Projects - Some QBO versions have a "Projects" feature. Factor can link to existing QBO projects, but the QBO API does not allow Factor to create them automatically. If your firm uses QBO projects, link Factor projects to any QBO projects already in use but move to the use of sub-customers for new Factor projects going forward.
When to Contact Support
Contact Factor support if:
The integration connection cannot be re-established
Invoices consistently fail to sync after verifying all mappings
Expense data is incorrect or orphaned and you cannot identify the cause
You see error messages you cannot resolve
When contacting support, provide your firm name, the specific records affected (invoice numbers, expense descriptions), and any error messages visible in Factor or QBO.