How to Switch Shopify Agency Without Breaking Your Store

What should you check before you switch Shopify agency?

Check who owns what. Before you tell your current agency you're leaving, confirm that you are the store owner, that the domain is registered to your business, and that apps and marketing accounts are billed to you. Fixing ownership is much easier while the relationship is still friendly.

In your Shopify admin, open Settings > Users. The store owner is listed at the top. If the owner is someone at your agency, that's the first thing to fix. Collaborator accounts are the norm for agencies, and Shopify doesn't let you transfer store ownership to a collaborator, so an agency should never need to own your store.

How do you take back store ownership from an agency?

Only the current store owner can transfer ownership, so the agency has to start it. On plans other than Plus, there are two routes, both described in Shopify's help center:

1. To an existing user: the owner goes to Settings > Users, opens their own profile, chooses Change ownership for the store and enters the new owner's email. The new owner must already be a user on the store, so add yourself as a staff user first.
2. To someone outside the store: the owner goes to Settings > General, clicks Manage in the Transfer store section and enters your email. You accept the store from the email you receive.

Things that can block or complicate a transfer: Shopify Capital or Shopify Credit, an active Shopify Balance account, and unpaid bills, which the new owner takes on. Custom domains need to be transferred too. Shopify Plus stores go through Plus Support instead.

If your agency built the store in its Partner dashboard and never transferred it, it's a client transfer store. They can transfer it to you, but Shopify Payments must be deactivated first and Shopify Capital, Credit or Balance can't be active.

Collaborator or staff account: which should the new agency use?

Use a collaborator account. Agencies request access with your 4-digit collaborator request code, you approve the permissions, and their access doesn't count toward your plan's user limit. Staff accounts are for your own team.

Give the new agency only the permissions the work needs. Shopify warns that collaborators can request every permission, so read the request before you accept. Inactive collaborators lose access after 90 days without logging in.

How do you hand over the theme code?

Get two things: a copy of the live theme and the version history. The copy protects you if anything goes wrong; the history tells the new agency why the code looks the way it does.

• Download the live theme. In Online Store > Themes, use the actions menu and choose Download theme file. Shopify emails a .zip to the address on your staff login.
• Duplicate the live theme and keep one copy untouched as a rollback point.
• Ask for the Git repository. If the agency used Shopify's GitHub integration, ask them to transfer the repository to your GitHub organization, or give you and the new agency write access. Shopify only lets organization members with write access connect branches.
• Ask about local or build tools. Some themes compile CSS or JavaScript from source files that don't live in Shopify. Without them, the next developer edits compiled files.

Also note which theme you're on and its version. Themes from the Shopify Theme Store can be updated; customized code may not carry over cleanly, so the new agency needs to know what was changed.

What happens to apps and custom apps?

Public apps from the Shopify App Store stay with your store, but check that each subscription is billed to you and that the app's own account (reviews, email, subscriptions) uses your email, not the agency's.

Custom apps need more care. Custom apps are now created and managed in the Dev Dashboard, while legacy custom apps created before January 1, 2026 are still managed from your Shopify admin. Shopify notes that apps created in the admin are tied to the staff or collaborator account that made them, and collaborators can't use the Dev Dashboard at all.

1. List every custom app, what it does and who created it.
2. Ask for the source code and hosting details of any app that runs on the old agency's servers.
3. On each legacy custom app's App settings page, change the account that receives warnings to someone at your company.
4. Plan to rotate API credentials or recreate the app under your own account, so the old agency's access ends cleanly.

Shopify's advice for apps whose developer you can't reach is to contact Shopify Support or hire a Shopify Partner.

What about the domain and DNS?

Make sure the domain sits in a registrar account you control, or in your own Shopify admin if you bought it through Shopify. Don't change DNS during the handover unless you have to.

If the old agency registered the domain, ask them to move it to your registrar account first. When DNS does change, copy every existing record before editing. Email (MX, SPF, DKIM, DMARC) and services like Google Search Console verification often live in the same zone, and they break quietly.

What documentation should you ask for?

Ask for a short handover document. It saves the new agency days of detective work, which you pay for either way.

• Theme name, version, and a list of custom sections and code changes.
• Apps installed, why each one is there, and their monthly cost.
• Custom apps, scripts, Functions and integrations (ERP, 3PL, accounting), with logins owned by you.
• Shopify Flow workflows and automations.
• Redirect rules, tracking setup (pixels, GA4, Google Tag Manager) and known issues.
• Marketing and analytics accounts: Search Console, GA4, Merchant Center, Meta Business, email platform.

Shopify agency handover checklist

How should the switch itself be timed?

Overlap the two agencies for a short period. The new agency reviews the store, theme and apps with collaborator access while the old one is still reachable for questions.

1. Secure ownership, domain and accounts.
2. Collect the theme, repository and documentation.
3. Give the new agency collaborator access and let them audit.
4. Agree on a cut-off date and avoid launches or sales around it.
5. Remove the old agency's collaborator access and rotate any shared credentials.

Our take: avoid switching in the weeks before a big sale or product launch. Most handover problems surface in the first few changes, and you want time to fix them.

How we can help

We take over stores built by other developers regularly, starting with a review of the theme, apps and access before we change anything. Start with a free Shopify audit, or see how our Shopify maintenance and support plans work once the handover is done.