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01Agent-first
Runs where you already work
Plug it into Claude, ChatGPT or Cursor. Describe the move in plain English; the agent runs it.
02Engineer-led
Our production engine, unlocked
The pipeline our engineers use on managed enterprise migrations — the same code, now something you can drive yourself.
03Pricing
Try 10 pages free, then $1 a page
Credit-based, pay-as-you-go. No scoping call, no quote — sample it on your own docs before you spend anything.
04Sources
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Merge & Consolidate Two Zendesk Instances with zero downtime

Fold one Zendesk org into another — deduplicate records, reconcile custom fields and IDs, and unify agent lists without losing history. Engineer-led, validated end-to-end.

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Last updated November 2026

COMPLETE COVERAGE

Intelligent Human-Verified Data Mapping

Our migration engineer precisely maps every data point from Zendesk to Zendesk, ensuring perfect continuity for your customer support operations.

Zendesk
Zendesk
Tickets
Tickets
Ticket Comments
Ticket Comments
Ticket Attachments
Ticket Attachments
Users
Users
Organizations
Organizations
Groups
Groups
Ticket Fields
Ticket Fields
Ticket Forms
Ticket Forms
User Fields
User Fields
Organization Fields
Organization Fields
Help Center Articles
Help Center Articles
Help Center Categories
Help Center Categories
Macros
Macros
Tags
Tags
Satisfaction Ratings
Satisfaction Ratings

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What Our Customers Say

Real migration stories

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CUSTOM MIGRATION

Fully customizable engineer-led migration

Tailor your migration from Zendesk to Zendesk exactly to your needs with our flexible customization options. Our experts will configure the perfect migration plan for your business.

Migration Filters

Ticket Status

Filter by open, resolved, closed, or pending states

Assignment Group

Migrate tickets assigned to specific support teams or queues

Priority Level

Select records based on urgency, impact, or priority levels

Time Range

Migrate tickets created or updated within a specific period

Data Types

Incidents & Requests

Active and closed tickets including history, comments, and attachments

Problems & Changes

Root cause analysis records and change management workflows

Assets & CMDB

Hardware, software, and configuration items with relationships

Knowledge Base

Help articles, FAQs, and internal documentation with categorization

ZERO DOWNTIME

Your timeline. Our engineers.

A dedicated engineer runs your migration, planned around your schedule and your data.

No babysitting a wizard. Avoid debugging errors yourself.

Looking for a more detailed migration timeline?

Contact our team

Speed

The migration timeline depends on both our turnaround time and yours.

We can complete a migration in under a day when the accounts are connected and the sample migration is approved promptly.

Background Sync

We also support migrating the newest records first, so you can go live faster while the rest of the data is synced in the background.

Data Volume Impact

Larger data volumes may require longer migration windows.

Continuous Operation

Weekend migrations minimize disruption to your customer service operations.

MIGRATION TIMELINE

Your Zendesk to Zendesk migration, step by step

See how long your migration will take from start to finish. Drag the slider to estimate based on your data volume.

How many records are you migrating?

<10K 50K 100K 250K 500K 1M 2M 5M 10M+
Checklist ~3 days
Sample 1 day
Review ~2 days
Full 2 days
Delta 1 day
Your team ClonePartner

Estimated total

~9 business days

1

Migration Checklist

1 day · ClonePartner ~2 days · Your team

We prepare the optimal data mapping as a shareable spreadsheet. Your team reviews, approves, and adds any customizations.

2

Sample Migration

1 day · ClonePartner

We run a test migration with a representative sample of your data to verify mapping accuracy and identify any potential issues before the full run.

3

Review & Approve

~2 days · Your team

Your team reviews the sample migration results, confirms data accuracy and mapping, and gives the go-ahead for the full migration.

4

Full Migration

2 days · ClonePartner

We execute the complete migration of all your data to your new Zendesk, with real-time progress tracking and comprehensive logging.

5

Delta Migration

1 day · ClonePartner

We capture and transfer any new data that was added or updated during the main migration to ensure no data is lost. This final sync keeps everything current.

Related Guides

Pros and cons of different migration options

Choosing the right approach is key because migrating from Zendesk to Zendesk isn't just about moving data – it's about protecting your service continuity and SLAs.

Feature / Criteria ClonePartner Automated Tools CSV Import In-house migration
Custom Scripting for complex data ✓ Engineers build & maintain ✗ No ⚠ Manual ✓ Yes – but costly
Sandbox & Pilot Migrations ✓ Full sandbox + pilot plans ⚠ Limited ✗ No ⚠ Often Informal
Manual validation & reconciliation ✓ Automated + manual QA ✗ No ✓ Yes (Manual) ✓ Heavy manual effort
Backup & rollback plan ✓ Robust procedures ✗ No ✗ No ⚠ Often incomplete
Handles automation and integrations ✓ Full support ⚠ Partial ✗ No ⚠ Possible but fragmented
Post-migration engineer support ✓ Dedicated engineers ✗ No ✗ No ⚠ Limited SLA support
Adaptable to API changes ✓ Proactive adaptation ✗ No ⚠ Manual fixes ⚠ Slower response
Turnaround / SLA predictability ✓ Predictable SLAs ⚠ Fast but brittle ⚠ Slow and manual ⚠ Often slower
Data Security & Compliance ✓ High – enterprise grade ⚠ Medium (depends) ⚠ Low (manual) ⚠ Hidden gaps common
Pricing predictability ✓ Transparent & fixed ⚠ Low (per-job) ⚠ Low (manual hours) ⚠ High/variable OPEX
End-to-end project management ✓ Full E2E delivery & PM ✗ No ✗ No ⚠ Often partial
Business impact & opportunity cost ✓ No diversion of staff ✗ No ✗ No ⚠ Diverts engineering

What does an Engineer-led migration mean anyway?

Speed & Accuracy: Our Blended Method

We blend automation (smart scripts, bulk APIs) with human expertise for speed without risk. Our engineers manually check every mapping, validation, and exception.

You get:

  1. Speed of automation for bulk record migration
  2. Precision of engineers verifying integrity and business logic
  3. Pilot migrations and sandbox testing to catch issues early
  4. Real-time validation reports and rollback readiness
Result: 50x faster migrations than manual imports — with near-zero error rates.

Handling the Tricky Tech and API Details

The Zendesk and Zendesk APIs each behave differently, which is where our engineers shine. We build custom logic to handle the data quirks where generic tools typically break.

We handcraft API logic for:

  1. Field mapping and transformation
  2. Pagination, rate-limit handling, and throttling
  3. Preserving incident history, worknotes, and CI relationships
  4. Syncing custom fields, SLAs, and workflows without breaking structure
Our scripts: Natively retry failed calls, re-queue large attachments, and ensure data parity.

No Guesswork

We don't just promise smooth migrations—we measure and prove them. Every client receives a Migration Validation Report with all metrics.

Typical results across projects:

  1. 100% record-count parity between your Zendesk data and Zendesk
  2. Zero downtime during staged cutovers
  3. 99.9% attachment integrity (verified via checksum)
  4. Full automation and preservation of all business rules
Our standard: Includes full SLA and CMDB-relationship preservation and 30 days of engineer-assigned support post go-live.

We Adapt to Your Setup (Not the Other Way Around)

No two teams configure Zendesk or Zendesk exactly the same way—with unique workflows and data. We customize every migration script to fit your exact workflow, SLAs, and CMDB relationships.

Our engineers adapt for:

  1. Custom fields, SLAs, and workflows
  2. Multi-brand or multi-language setups
  3. Historical imports and partial (date-based) migrations
  4. Integration re-mapping for CMDB, monitoring, or chat tools
The promise: If your data doesn't fit a standard template, we build one just for you.

Enterprise-Grade Security & Compliance

Your customer data is precious. Our migration process maintains the highest standards of security and regulatory compliance.

SOC 2 Type II

Independently audited compliance with rigorous security standards

ISO 27001

Certified information security management system

GDPR

Full compliance with EU data protection regulations

HIPAA

Certified for handling protected health information

AES-256 Encryption

Bank-grade encryption for all stored credentials

Latest TLS

Secure transfer protocol for all data in transit

Role-Based Access

We follow role-based access control for every migration project

Scheduled Deletion

Automatic data purging after migration completion

FAQ

Frequently Asked Questions

Everything you need to know about consolidating two Zendesk instances. Can't find what you're looking for? Talk to our team.

Still have questions?

Book a free 30-minute consultation with our team.

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Zendesk consolidation

5 questions
How do you merge two Zendesk instances without losing data?
We connect to both Zendesk instances, map every record between them, deduplicate overlapping entries, and reconcile IDs and any custom fields. Both instances stay live during the migration; we cut over only after validation passes.
What happens to duplicate records when consolidating Zendesk instances?
Duplicates are detected on a match key you choose, for example an email address, an external ID or a custom field, depending on the records involved. We surface a dedup report before cutover so you can confirm merge-vs-keep decisions. No record is silently dropped: every duplicate is either merged, kept as-is, or flagged for manual review.
How are record IDs reconciled across the two Zendesk instances?
IDs almost never line up across instances. We build an ID map during the sample run and rewrite references, such as parent and child records, attachments and other linked records, so relationships survive the merge. The map is exported as a CSV for your records after cutover.
What if our two Zendesk instances are set up differently?
We inventory how both instances are set up before the migration, including any custom fields, workflows and automations. Missing fields you want to keep are created in the instance you are consolidating into, conflicting fields are reconciled per your direction, and workflows are ported or rebuilt so the consolidated instance behaves the way your teams expect.
What does post-merge cleanup involve for Zendesk?
We hand over the ID map and dedup report, and document the new field layout. Any issue found after the merge is covered by our post-migration support, so you can decommission the old instance with confidence.

Before you start

4 questions
Do I need professional help for this migration?
Yes. Professional help ensures proper field mapping and preservation of relationships between records. Our engineer-led approach catches edge cases that automated tools miss.
Does ClonePartner provide guidance before committing?
Yes. We provide a free consultation and assessment. We'll review your data structure, discuss your requirements, and provide a detailed migration plan and fixed-price quote before you commit to anything.
Do you use an off-the-shelf tool to consolidate our Zendesk instances, or is this built for our data?
It is built for your data. Each migration is a set of custom scripts written for your data model, not a generic import tool. That is also why we start with a sample migration: you see your own records in the instance you are consolidating into before the full migration is committed.
Can we see a sample merge of our Zendesk data before the full merge runs?
Yes. We run a sample migration on your own data first, so you can review how the merged records look before the full migration goes ahead. We run validation scripts to check the record counts against the instance being merged in; if a field is missing or mapped wrong, or anything else needs adjusting, we fix it in the migration scripts and re-run the sample as many times as you need. The full migration only runs after you've approved the sample. On projects delivered in phases, each phase gets its own sample migration for you to approve.

Data & mapping

13 questions
Will the original assignees, message authors and created dates be preserved when the instances are merged?
Yes. Created-time metadata is carried across, and so are assignees and message authors who have a user account in the instance you are keeping. Where one of them cannot be set natively on the migrated record, it is kept as embedded metadata on that record.
Do tags and macros migrate along with tickets, or only the tickets themselves?
Both can come across. Tags on your tickets carry over as part of the ticket data, in the sample migration and the full one. Macros can be migrated as well. You decide the scope with us, so either one can also be left behind.
What happens to tickets in the other Zendesk account assigned to agents who have left or don't have an account in the one we are keeping?
They still come across. Before the migration runs, you decide where they go: to a fallback owner you choose, or left unassigned where Zendesk allows it. Either way, each ticket can get a tag with the original agent's name, for example Assigned_to_Jane, so your team can still see and filter who handled it and reassign them later.
Will consolidating our Zendesk instances send emails or notifications to customers, our team or anyone else?
No. Before the sample or full migration starts, we confirm with you that nothing in the instance you are consolidating into will send messages about the migrated data: we import with notifications switched off wherever Zendesk allows it, and pause any automation that could send them or give it a condition that skips migrated records. We only proceed once you have confirmed it. If you want anyone told about the move, that message is sent separately, once the migrated data has been checked.
Can you migrate data that Zendesk can't take in through an API?
In many cases, yes. Where something can't be written through an API, we recreate it through Zendesk's user interface where the interface allows it, and where that work is repetitive we script and automate it. We tell you up front which items are handled this way, because recreating them through the interface can add time to the schedule.
What if the instance we're consolidating into requires fields our other Zendesk instance doesn't fill?
We check the instance you are consolidating into for required fields the incoming data cannot fill and bring each one to you before those records are migrated. Together we agree how each one is handled, such as a mapping from an existing field, a default value, or, where that instance lets the field be made optional, setting it to not required for the migration so you can make it required again once the migration is complete. The migration then runs with that rule applied, so no records are rejected or left behind.
How will we tell migrated records apart from the ones already in our Zendesk instance?
We can mark every migrated record in the instance you are consolidating into, for example with a custom checkbox field that names the instance it came from, so your team can tell migrated data apart from records created there. We agree the marker with you during scoping so it fits how your team uses that instance.
We use a lot of custom fields in both Zendesk instances. Can you map them across?
Yes. Each migration is a custom script written for your project, so custom fields in the instance being merged in are mapped to the fields in the instance you are consolidating into. Where the same field has a different type in each instance, such as text in one and a number in the other, the script converts it. We agree the mapping with you and prove it on a sample migration before the full run.
One of our Zendesk accounts is closing soon. Can you work from its JSON export instead of the live account?
Yes. We can migrate from Zendesk's admin JSON export, so that account doesn't need to stay open for the whole move. We download the attachments on ticket comments before the account closes and upload them with the tickets they belong to.
Can you bring our Zendesk Talk call recordings across when we merge our Zendesk accounts?
Yes. Call recordings attached to your Zendesk tickets are exported through the Zendesk API and moved with the tickets they belong to. We agree with you in the data mapping how they will appear in your main account, and you check them in the sample migration before the full run.
Will our ticket formatting carry over when we merge Zendesk accounts?
Ticket content goes into the account you are keeping in the format Zendesk already uses, and the sample migration lets you compare migrated tickets side by side with the originals before the full run. If anything renders differently, such as HTML appearing as raw text, we adjust the script and re-run the samples until you sign off.
Do you migrate changes, problems and tasks as well as tickets when we merge Zendesk instances?
Yes, where Zendesk supports them. Changes, problems and tasks can be migrated along with their notes, attachments and approvals, not just your tickets.
Can you migrate CMDB and asset records along with tickets when we merge Zendesk instances?
Yes. Asset and CMDB records can be part of the same migration as your tickets, along with your knowledge base articles, wherever Zendesk's API supports them. We confirm in the migration checklist which asset types come across and where each one maps in the instance you keep, and you check them in the sample migration before the full run.

Timeline & downtime

3 questions
How long does consolidating two Zendesk instances take?
Most migrations complete within 1–5 business days, depending on data volume and complexity; very large migrations, such as several hundred thousand records, take longer. We provide a detailed timeline after the initial assessment and can often complete small migrations in under 24 hours.
Will there be downtime while we consolidate our Zendesk instances?
No. Our migration process is designed for zero downtime. Both Zendesk instances stay available to your team throughout: the bulk migration runs in the background and the cutover is fast, so your team keeps working.
How do you avoid duplicate tickets when we move a support address from one Zendesk account to the other?
We agree one cutoff time with you, lined up with when the address is moved. Everything received in the account you are merging in up to that moment is migrated, and everything after it arrives directly in the account you are keeping. Both Zendesk accounts can stay live side by side, as long as each one is connected to its own support email addresses so incoming mail lands in only one place. Once the support email of the account you are merging in is connected to the account you are keeping, and tickets are arriving there directly, a sync run after that point can pull in the same tickets a second time, so we time the final sync around your email cutover and flag it if a sync you ask for falls after your switchover point. The final list of migrated tickets with their new IDs lets you check the boundary and spot any ticket that came in around the switch.

Security & access

1 question
Can we whitelist a single IP instead of opening our network to your migration tool?
Yes. All migration traffic runs through a centralized system using one fixed IP, which your IT team can whitelist instead of opening broader network access.

Pricing

1 question
Is migration pricing a flat fee, or does it scale with data volume?
It's a flat fee with no hidden costs. The price we agree with you for your scope is the price you pay, and small variances in the final volume, a bit more or less, are included.

After go-live

7 questions
How do I validate that everything migrated correctly?
Every client receives a Migration Validation Report with comprehensive metrics including record-count comparison, attachment integrity verification via checksum, and full audit logs of the migration run, showing every record created, skipped or failed. If any item didn't come across, the report names each one, the specific reason, and how to bring it across if you want it there. We also offer unlimited sample migrations, so you can check your data before the full migration runs.
What support do you provide after the migration goes live?
At ClonePartner, we consider ourselves your partners in this journey. We take full accountability for your migration's success. Once your migration goes live, we provide 30 days of comprehensive post-migration support as standard, and longer support, such as 60 or 90 days, can be agreed for your project. During this period, we help with anything related to your migrated data, so your migration is a complete success.
Will we get a migration report and a mapping sheet linking old record IDs to new ones?
Yes. We provide a comprehensive migration report along with an ID-mapping sheet that links each record's old ID to its ID in the instance you are consolidating into. This ensures full traceability, simplifies post-migration verification, and helps your team validate that records have been migrated accurately.
After migration, do I contact ClonePartner or the platform's own support if something looks wrong?
ClonePartner is the contact for anything about the migrated data itself. Questions about the platform itself, such as how its features and settings work, go to the platform's own support or to whoever administers it for you.
Will inline images and signatures in merged tickets break once we shut down the Zendesk account we merged from?
File attachments that we migrate are rehosted in the Zendesk account you are keeping. Inline images embedded directly in email bodies, including signatures, are migrated as they are, so they can keep being served from the account you merged from and appear broken once it is deactivated. If this matters to you, we can identify the affected tickets and, before you shut the other account down, reimport the ones your team has not changed since the merge with their images rehosted in the account you are keeping.
If a merged ticket has to be deleted and reimported to fix an issue, does it lose its original dates or history?
No. A ticket reimported to fix an issue, such as broken inline images, keeps its original creation time and its conversation history with the original timestamps. Tickets your team has changed since they were merged into the account you are keeping are left out of any reimport, because overwriting them would lose those updates.
Can a ticket merged in from our other Zendesk account be reopened later if a customer or agent needs it?
It depends on Zendesk and on the status the ticket arrives with. You choose the status migrated tickets come in with, such as closed for old history, and if you later want tickets set differently we can update them in bulk. Whether an agent can reopen a ticket that arrived closed, or move it from an archive area back into a live one, depends on how Zendesk handles closed tickets, so we check that with you during scoping and can test it on a sample ticket before go-live.

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Zendesk Migration?

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Attention to Detail

We meticulously handle every aspect of your migration, ensuring no data is lost during transfer and mapping every field correctly between platforms.

Custom Solutions

Every business is unique. We tailor your migration strategy to match your specific requirements, workflows, and data structures.

Security & Compliance

Your customer data is handled with enterprise-grade security protocols, ensuring compliance with GDPR, HIPAA, and industry standards.