Intuit and QuickBooks are registered trademarks of Intuit Inc. used with permission.
When you move your company file from QuickBooks Desktop to QuickBooks Online, your existing integration links need to be rebuilt, whether you have been using the CORE–QuickBooks Desktop integration utility, or you moved from BillQuick to CORE and had been using BillQuick's QuickBooks Desktop sync. QuickBooks Online assigns its own internal ID scheme to every client, project, invoice, payment, and other record, which is different from the ID scheme used in QuickBooks Desktop. Because of this, the record-to-record links your prior integration relied on do not carry over automatically. They need to be reviewed and reconfigured against your new QuickBooks Online company file before the integration can go live again.
You have two options for handling this. Review both, along with their requirements, before choosing one.
If you have questions about which option is right for your company, please contact your Account Manager or submit a support ticket.
Option 1: Backend Cleanup (Free)
Option 2: Consulting-Led Link Migration (Paid and managed service)
Option 1: Backend Cleanup (Free)
BQE runs a backend cleanup process that removes all outdated CORE–QuickBooks Desktop links, clearing the way for you to start using the CORE–QuickBooks Online integration.
What BQE handles:
- Running a backend cleanup process that removes all outdated links in CORE.
What you handle:
After the cleanup, you are responsible for manually remapping:
- Master records (clients, projects, vendors, and similar)
- Active projects
- Open invoices
- Payments
- Any other CORE data associated with the previous QuickBooks Desktop integration
Note: This option does not preserve any of your existing linkages. Every record needs to be remapped manually on your end, so plan for a significant time investment.
Option 2: Consulting-Led Link Migration (Paid and managed service)
This is a fully managed service. BQE's Consulting team migrates your existing CORE (or BillQuick)–QuickBooks Desktop links into your new CORE–QuickBooks Online environment on your behalf.
To use this option:
- Contact your Account Manager to request the service. You will get a formal quote based on your company's setup.
- Turn off the QuickBooks Online Projects feature. With Projects off, your QuickBooks Desktop jobs transfer into QuickBooks Online as sub-customers, which is the supported behavior for this integration. QuickBooks Online Projects are not supported within the CORE–QuickBooks Online integration.
- Complete your QuickBooks Desktop to QuickBooks Online migration. BQE strongly recommends using the QuickBooks conversion tool for this step, and your data must be fully transferred before the link migration can begin.
- Review and approve the formal quote.
- Grant BQE Administrator access to your QuickBooks Online account by adding support@bqe.com as an admin user. If you are currently using MongoDB with the QuickBooks Desktop Integration utility to send data between CORE and QuickBooks Desktop, also share your MongoDB credentials so that the connection can be carried over.
- Notify BQE when the access is granted and payment is complete. A support ticket is created at that point, and the migration typically takes 5 to 7 business days.
What BQE handles:
- Retrieving your existing linkage data.
- Re-establishing the appropriate links between CORE and QuickBooks Online.
- Managing the link migration end-to-end on your behalf.
After the migration: BQE meets with you for a couple of one-hour sessions covering an overview of the CORE–QuickBooks Online integration, including navigating the relevant menus, how synchronization works, and other key functionality.
Frequently Asked Questions
What needs to be done in CORE to disconnect or discontinue the existing QuickBooks Desktop integration?
You can simply stop using the CORE–QuickBooks Integration utility with QuickBooks Desktop, or uninstall it completely.
After the Desktop file has been migrated to QuickBooks Online, what steps are required to connect CORE to the new QuickBooks Online company?
CORE needs to be connected to QuickBooks Online. This is handled during the follow-up sessions.
Will the follow-up sessions include an overview of the new CORE–QuickBooks Online integration process, a review of required settings or mappings, and recommendations to help prevent duplicate customers, projects, invoices, or other transactions before the initial sync?
Yes. All of this is covered during the follow-up sessions.
What are the main differences between the CORE–QuickBooks Desktop integration and the CORE–QuickBooks Online integration?
See Comparing QuickBooks Desktop and QuickBooks Online integrations in CORE for a full breakdown.
Does BQE validate that CORE clients, projects, invoices, payments, vendors, and vendor bills are properly linked to the corresponding QuickBooks Online records as part of the service?
Yes. After the links are migrated, BQE validates the mapping between your CORE records and their corresponding QuickBooks Online records. Master data is prioritized first: clients, projects, employees, and vendors are reviewed and mapped in close coordination with your team.
Transactional records generally map well when the same IDs exist in both the original integration and the resulting QuickBooks Online file. Where those IDs differ, some older invoices and payments may remain unmapped. This is an expected outcome and does not affect ongoing operations. The follow-up sessions cover best practices for this situation, including date filters that keep historical transactions from syncing and creating duplicates in QuickBooks Online.
Should a cutoff time be established, instructing staff not to send or sync invoices or other information from CORE to QuickBooks once the migration to QuickBooks Online begins?
Yes, this is highly recommended. Notify BQE when your data has been fully transferred from QuickBooks Desktop to QuickBooks Online and you have granted access to your QuickBooks Online file. A ticket will be created at that point, with an estimated turnaround of 5 to 7 business days.
Can my team continue working in CORE and QuickBooks Online while BQE performs the link migration?
Yes. During the migration, you can continue working in QuickBooks Online on standalone accounting activities, such as issuing checks or other accounting-related tasks unrelated to the CORE integration.
However, any records or transactions related to the CORE integration that are created directly in CORE or QuickBooks Online after the designated cutoff date will not be included in the migration mapping process. If applicable, these items are reviewed and addressed during the follow-up sessions.
Does the service include reconciliation between CORE and QuickBooks Online after the migration (for example, A/R, invoices, payments, and vendor bills)?
No. This service does not include any account reconciliation activities. Its scope is limited to the integration link migration and the follow-up sessions, which cover an overview of the CORE–QuickBooks Online integration, key menu navigation, synchronization processes, configuration options, and other essential functionality.
If the migration creates or identifies duplicate or incorrectly linked records, is correcting those issues included in the managed service?
Yes, BQE can assist with duplicate links or incorrectly linked records. These are typically identified and resolved prior to final delivery, because the migration process requires a strict one-to-one mapping between records.
This does not extend to duplicate records within your resulting QuickBooks Online company file itself (for example, duplicate clients, projects, vendors, or other master records created in QuickBooks Online). Addressing and consolidating duplicates within QuickBooks Online falls outside the scope of this service.