TL;DR
- You can deduplicate HubSpot and Salesforce while they sync if each merge covers both CRMs.
- Merging companies in HubSpot doesn't merge the linked accounts in Salesforce.
- A duplicate left active in the other CRM can come back on the next sync.
- HubSpot merges can't be undone, and Salesforce's Recycle Bin keeps merged-away records for 15 days.
- Dedupely cleans HubSpot and Salesforce, merging synced duplicates in both CRMs in one action.
Yes, you can deduplicate HubSpot and Salesforce while the integration keeps syncing. The condition is that each merge happens in both CRMs at once. A merge on only one side leaves the matching record active on the other, and the next sync can bring the duplicate back.
That's why cleaning a synced pair often turns into manual work. Someone merges in HubSpot, fixes Salesforce by hand, and some duplicates slip through along the way.
In this post, you'll see what each CRM does when you merge on one side and why merged records come back. You'll also see what to look for in a tool for several CRMs, and what to settle before merging.
What happens when you merge on only one side
The integration keeps a HubSpot record and a Salesforce record in sync. A merge changes one side of that pair, and each CRM's help pages describe what happens to the other side.
| Where you merge | What happens to the synced record |
|---|---|
| Contacts in HubSpot | Only the primary contact keeps syncing. The Salesforce record linked to the secondary contact stops syncing to HubSpot. |
| Companies in HubSpot | The Salesforce accounts aren't merged. The surviving company keeps syncing with its linked account. On the older version of the integration, companies can't be merged at all. |
| Leads or contacts in Salesforce | If deletion is turned on, the HubSpot contact linked to the secondary record is deleted. If the primary isn't the record syncing with HubSpot, the HubSpot contact stops syncing until you resync it. |
As of October 2026, from HubSpot's knowledge base: Merge records, Sync companies between HubSpot and Salesforce and Resolve duplicate Salesforce records syncing with HubSpot.
In several of these cases, one CRM ends up with a record the other no longer matches. That record is still active. Depending on your sync settings, the next sync can re-create the duplicate or overwrite the values you kept in the merge.
Why merged records come back after a sync
When a duplicate returns after a merge, the cause is often on the other side of the sync. These situations come up often.
- A leftover record in the other CRM: the duplicate was merged in one CRM, while its match in the other is still active.
- Two Salesforce records with one email: Salesforce allows two leads or contacts with the same email address, and HubSpot doesn't. HubSpot syncs with whichever one was updated most recently in Salesforce.
- Company matching that only applies to new records: the company sync matches companies on mapped field values. That matching only applies to companies and accounts created after the sync is turned on.
- Deletion settings: deleting a HubSpot company doesn't delete its Salesforce account. In the other direction, you choose whether a deleted Salesforce account deletes its HubSpot company.
As of October 2026, from HubSpot's knowledge base: Resolve duplicate Salesforce records syncing with HubSpot and Sync companies between HubSpot and Salesforce.
What counts as a duplicate is also case by case. A parent company and a subsidiary can share a domain and still be two accounts your team wants to keep.
Common workarounds and where they fall short
Teams that clean a synced pair without merging on both sides tend to use one of these approaches. Each one helps with part of the problem.
| Workaround | What it solves | What it leaves open |
|---|---|---|
| Merge in one CRM, fix the other by hand | Works for a handful of records | Slow at scale, and some pairs get missed |
| Pause the sync while you clean | Stops records from moving during the cleanup | The leftover records are still there when the sync resumes |
| Change integration settings or permissions | Can stop some new duplicates from being created | Existing duplicates stay in both CRMs |
| Custom fields or code to track a master record | Fits your exact setup | Someone has to build and maintain it |
| Clean both databases in spreadsheets | Shows both datasets side by side | The files go stale as soon as either CRM changes |
Each of these handles one side of the sync, or one moment in time. What keeps the pair linked is a merge that changes both records together.
Can one tool deduplicate more than one CRM?
Yes. Deduplication tools can connect several CRMs, and when two of them sync, a tool can merge a duplicate in both at once. Those are two different jobs, so it helps to know which one you need.
Cleaning each CRM on its own
When separate teams, regions or brands each run a CRM, each one collects its own duplicates. A customer in two CRMs isn't always a duplicate, because it depends on what each system is for. Our post on managing duplicates across more than one CRM covers how to decide.
Merging a synced pair in both CRMs
When HubSpot and Salesforce sync, the same customer exists in both on purpose. A merge there has to change both records, or the link between them breaks. Syncs are one of several ways duplicates reach a CRM, alongside the imports and integrations covered in deduplication across connected tools.
What to ask before you choose a tool
- Does it detect the sync and merge the matching records in both CRMs in one action?
- What happens to a synced record when only one of the two CRMs is connected?
- Are the contacts, deals and activity attached to a record kept in both CRMs?
- Does it need custom fields or workflow changes to work with the sync?
- Is every merge logged, with the original values available to export?
What to settle before you merge synced records
A merge across two CRMs changes data that two teams rely on. A few decisions up front keep it predictable.
Decide which value wins
Agree on the winning value for fields both CRMs care about, like owner, lifecycle stage and address. Sales may own some fields in Salesforce while marketing owns others in HubSpot.
Start with the obvious duplicates
Begin with exact matches on the field that identifies each record, like email for contacts or domain for companies. Leave branches, subsidiaries and shared inboxes for review, since your team may want them apart.
Keep the original values
HubSpot's knowledge base says records can't be unmerged. By default, the merged record gets a new Record ID, and both records leave their active workflows. Only portals in HubSpot's opt-in Primary ID Preservation for Merged Records beta keep the primary's ID, and there the primary stays enrolled. In Salesforce, the merged-away record goes to the Recycle Bin, where deleted items stay for 15 days. Restoring it from there doesn't change the master record.
As of October 2026, from HubSpot's knowledge base: Merge records. From Salesforce Help: Recover Merged Salesforce Contacts and Manage the Recycle Bin in Lightning Experience.
Keep a record of the original values before you merge, with each record's ID in both CRMs. Our guides to HubSpot deduplication and Salesforce deduplication cover how each CRM merges on its own.
Check permissions in both CRMs
Whoever runs the merge needs the right to merge records in HubSpot and in Salesforce. A merge that works in one CRM and fails in the other leaves you with the same broken pair you started with.
How Dedupely merges synced HubSpot and Salesforce duplicates
Dedupely detects an active HubSpot–Salesforce Integration. Once you link the two CRMs in your CRM Settings, it merges the matching records in both CRMs in one action. There are no custom fields or workflow changes to set up, and the next sync doesn't re-create the merged duplicate.
Merges can't be undone, because they happen directly in your CRM and most CRMs can't undo them either. If the other CRM isn't connected, the merge is blocked. Dedupely stops anything that could break the sync unless you tell it to move forward. Every merge is in Merge History, and its CSV keeps the original data and record IDs. Merges made in both CRMs at once can't be undone, nor can company merges in a synced portal. Our guide to merging with an active HubSpot-Salesforce Integration covers the setup. Our HubSpot–Salesforce sync page covers the rest. See how to undo a merge.
One merge, two CRMs
The HubSpot–Salesforce integration keeps two records in step, so a duplicate lives in both CRMs. A merge on one side changes only half of that pair. The record left behind stays active, and depending on your settings, the duplicate can return on the next sync.
Deduplicating with the sync on comes down to merging both sides together. Decide which values win, start with the obvious matches and keep the original values, since merges in either CRM are hard to reverse. Then each customer ends up as one record in HubSpot and one in Salesforce, still linked.
Frequently asked questions
Can you merge duplicates while the HubSpot–Salesforce integration is on?
Yes, as long as the merge covers both CRMs. A merge in only one CRM leaves the matching record active in the other, and the next sync can bring the duplicate back. If you merge in Salesforce, HubSpot's knowledge base advises keeping the record that's currently syncing as the primary.
Why do merged records come back after a HubSpot–Salesforce sync?
The duplicate is often still active in the other CRM. Merging in HubSpot doesn't merge the linked records in Salesforce, so the leftover record can sync back. Two Salesforce leads or contacts with the same email, which Salesforce allows and HubSpot doesn't, can also keep a duplicate alive.
Does merging companies in HubSpot merge the accounts in Salesforce?
No, according to HubSpot's knowledge base: company merges in HubSpot don't merge records in Salesforce, and the other Salesforce account stays where it is. The surviving HubSpot company keeps syncing with its linked account. On the older version of the integration, companies can't be merged in HubSpot at all.
Can you undo a merge in HubSpot or Salesforce?
HubSpot's knowledge base says records can't be unmerged, and by default the merged record gets a new Record ID. In Salesforce, the merged-away record sits in the Recycle Bin for 15 days and can be restored. Restoring it doesn't affect the master record. Save the original values and record IDs from both CRMs first.
Should you pause the HubSpot–Salesforce sync to remove duplicates?
Pausing stops records from moving while you work, but it doesn't merge anything in the other CRM. When the sync resumes, the records you left behind are still active and can bring duplicates back. Merging the matching records in both CRMs together keeps the pair linked without pausing.
Or sign up with Google
Pipedrive Marketplace 
