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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). |
Same behavior as QuickBooks Desktop. 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 utility. 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:
|
| Project ID | The colon symbol (:) is allowed as part of the Project ID. However, we recommend avoiding colons and other special characters in Project IDs whenever possible, because the integration utility may display them incorrectly or, in some cases, prevent the project from syncing successfully. | The colon symbol (:) is not allowed as part of the Project ID. Colons and other special characters are not supported by this integration because they prevent records from syncing. See the list of acceptable characters in QuickBooks Online. |
| Project Display | Follows your CORE Project Display As settings. Select a project display option that clearly identifies any phase that will be synced. To ensure uniqueness and visibility, place the portion of the name that differentiates the phase at the beginning of the Project ID, because QuickBooks Desktop may truncate long project names. | Sends Project ID + Project Name regardless of the Project Display As settings. As a result, if the Project ID and Project Name are identical, the sub-customer in QuickBooks Online can display the name twice (for example, “Project A-Project A”). To avoid confusion, use distinct values for the Project ID and Project Name whenever possible. |
| CORE Project Phases | Sending CORE project phases is strongly recommended, but it is optional when syncing invoices and payments. However, if your workflow requires syncing employee reimbursable expenses or time entries (for QuickBooks Desktop Payroll purposes only), project phases must be synced. | Sending or mapping CORE project phases is mandatory, even to sync joint invoices or payments. |
| Taxes on CORE Invoices | The tax amount is always sent as a separate line item on the QuickBooks Desktop invoice. There is currently no setting available to prevent this behavior. As a workaround, we recommend deleting the tax line item from the QuickBooks Desktop invoice and allowing QuickBooks Desktop to calculate the sales tax automatically based on its tax configuration. |
QuickBooks Online (US): The tax amount is always sent as a separate line item on the QuickBooks Online invoice. There is currently no setting available to prevent this behavior. As a workaround, we recommend deleting the tax line item from the QuickBooks Online invoice and allowing QuickBooks Online to calculate the sales tax automatically based on its tax configuration. QuickBooks Online (Canada): CORE includes an option to prevent sending the tax amount as a line item on the QuickBooks Online invoice: Do not send MST/MET/Items Taxes as a line item to QuickBooks. We recommend turning on this option in CORE and allowing QuickBooks Online to calculate the sales tax automatically based on its tax configuration. |