1. CORE Help Center
  2. Getting Started
  3. Best Practices
  4. Integration

Comparing QuickBooks Desktop and QuickBooks Online integrations in CORE

Updated

Intuit and QuickBooks are registered trademarks of Intuit Inc. used with permission.

BQE CORE supports data integration with both QuickBooks Desktop and QuickBooks Online. While both integrations let you sync clients, projects, time entries, invoices, and payments between CORE and QuickBooks, there are meaningful differences in how each integration is set up and how specific records are handled.

Key Differences

The table below outlines the key differences between the CORE–QuickBooks Desktop and CORE–QuickBooks Online integrations.

Feature CORE – QuickBooks Desktop CORE – QuickBooks Online
Payroll Support Payroll settings can be configured directly within the integration. Payroll settings are not managed within the integration. Time entries can be sent for payroll processing, but setup must be completed directly with QuickBooks Online Support.
Client & Project Structure Supports Customers and Sub-customers (Jobs).

Includes Customers, Sub-customers (Jobs), and QuickBooks Online Projects.

Note: QuickBooks Online Projects are not supported within this integration.
Setup Requirements Requires installing an integration utility (middleware) on each computer used for syncing. No additional software is required. When connected, the integration is available to all users with the appropriate permissions.
Joint Invoice
(Mapping Requirements) 		Only the parent project is required to be mapped to send a joint invoice; phases are optional. Both the parent project and phases must be mapped before a joint invoice can be synced.
Joint Invoice
(Invoice Behavior) 		Invoices are saved at the Parent or Client level only. Saved as a single invoice at the Parent or Client level (recommended for simplicity), or split into multiple invoices by phase (for example, Inv2026_1, Inv2026_2, Inv2026_3).
Income Account Assignment
(Summarized Invoices) 		Driven by CORE configuration. The accounts displayed in the Invoice Journal in CORE will be the ones impacted in QuickBooks Desktop. Driven by Sync Settings (Default Accounts, Projects, Items).
Income Account Assignment
(Detailed Invoices) 		Driven by QuickBooks Desktop configuration. The accounts displayed on QuickBooks Desktop Items are the ones impacted. Same behavior as QuickBooks Desktop.
Expense Account Mapping Driven by QuickBooks Desktop configuration. The accounts displayed on QuickBooks Desktop Items are the ones impacted. Same behavior as QuickBooks Desktop.
Retainer Payments Applied Retainer payments applied after the invoice is created are transferred to QuickBooks Desktop as discounts. The invoice appears as paid and the original invoice line details remain unchanged. A CORE Retainer Charge item is added directly to the invoice to reflect the applied retainer, ensuring the invoice shows as paid within QuickBooks Online.
Sending Options

There is only one way to send records, managed through the QuickBooks Desktop Integration Tool. Record transmission is controlled through filter options within each module.

Note: The Send to QuickBooks options visible in CORE screens are intended for QuickBooks Online integrations and do not apply to QuickBooks Desktop.

Three methods are available:

  • From the main Integrations screen, primarily for batch synchronization.
  • From individual module screens (such as Client, Project, or Invoice) by selecting up to 25 records and using Send to QuickBooks under the Actions button.
  • From individual screens using the row-action menu for single-record sync.
Project ID The colon symbol ( : ) is allowed as part of the Project ID. The colon symbol ( : ) is not allowed as part of the Project ID.
Project Display Follows your CORE Project Display As settings. Sends Project ID + Project Name regardless of the Project Display As settings in CORE.

Related articles