Changing Shopify agencies can often expose years of undocumented code, forgotten credentials, mystery webhooks, abandoned apps, and complex integrations held together by one developer’s institutional memory. 

This makes the difference between an easy agency switch and a stressful mess often highly dependent on the handover process. A proper Shopify agency handover checklist should cover much more than giving a new partner access to Shopify Admin. 

The incoming agency needs to understand who controls the store, where the source code lives, how changes reach production, which custom apps and integrations are business-critical, what technical debt already exists, and how support incidents will be handled after the transition. 

When planning to switch Shopify agencies, start by securing merchant ownership and access, documenting the existing technology stack, auditing code and integrations, transferring operational knowledge, and giving the incoming agency a short stabilization period before major development begins. 

A thorough handover can reduce the discovery work your new agency needs to do and make its technical audit more efficient. It also gives the incoming team a clearer picture of where to focus first, so important fixes and higher-value projects can move forward sooner.

In this blog, we’ll break down everything you need to know about switching agencies and provide a Shopify agency transition checklist to make sure the process is as easy and painless as possible. 

Why Switching Shopify Agencies Is a Technical Project

Businesses change agencies for all kinds of reasons: Response times may have slowed, the store may have outgrown the original development team, technical debt may be piling up, internal priorities may have changed, or the business might simply need a Shopify support agency with deeper experience in integrations, Shopify Plus, POS, B2B, performance, or ongoing optimization.

Mature Shopify stores are often the sum of all the integrations and customizations holding them together. Orders might flow into an ERP, inventory could come from multiple warehouses, product information may originate in a PIM, Shopify Functions may control discounts or pricing logic, custom apps can power anything from bundles to fulfillment, while webhooks can trigger workflows outside Shopify entirely.

If you miss any of those dependencies during a Shopify store takeover, your checkout, inventory, fulfilment, analytics, promotions, or customer communications can break down. 

That is why an agency handover needs to be handled methodically and carefully to ensure nothing gets lost during the transition. 

Shopify Agency Handover Checklist: What to Transfer

A technical handover should answer three basic questions for every important system:

1. Who owns it?

2. Who has access to it?

3. What breaks if it stops working?

This sounds simple but usually ends up being more complicated than it appears. Here’s everything you need to know about handing over your store to a new agency for a smooth transition. 

1. Shopify Store Ownership and Collaborator Access

Let’s start with the basics. The merchant should normally retain ownership of the Shopify store when changing agencies. Switching partners doesn’t require transferring store ownership to the incoming agency. 

Instead, the new agency can request the permissions it needs through a Shopify collaborator account. Collaborator accounts let merchants control which areas of the store a partner can access, and they don’t count toward the store’s user limit. You can also remove access through Shopify Admin.

Shopify requires Partners to use two-step authentication with collaborator accounts. Collaborators also can’t access the Shopify POS app or the Point of Sale channel in Shopify Admin, so merchants that need an agency to work directly with POS should plan the necessary access separately.

During the handover:

1. Confirm that the correct person within the merchant organization owns the store.

2. Audit existing staff and collaborator accounts.

3. Give the incoming agency only the permissions it needs to do its work.

4. Confirm access before removing the outgoing agency.

5. Remove obsolete accounts once the transition is complete.

6. Review access to billing, domains, payments and other sensitive areas separately.

Above all else, don't remove access until you've identified and addressed all dependencies. 

2. Git Repositories, Theme Code and Deployment Workflows

Handing your ecommerce store over to another agency goes way beyond adding them to your Shopify platform. The new agency also needs to know where the authoritative version of all your code lives. 

Document:

• GitHub, GitLab or other repositories

• Repository ownership

• Production and development branches

• Pull request and approval processes

• Continuous integration or deployment workflows

• Local development instructions

• Build tools and dependencies

• Published and unpublished Shopify themes

• Theme naming conventions

• Release and rollback procedures

Shopify offers a GitHub integration that can connect repository branches to published or unpublished themes. Changes made to connected themes through the Shopify Admin can also be committed back to the associated GitHub branch. 

If you don’t use Shopify’s native GitHub integration, document the version-control and deployment workflow you do use. As part of the handover, the incoming agency should still verify that the production theme matches the repository or branch considered the source of truth.

If developers have been making emergency edits directly in Shopify without reconciling them with version control, the repository and production store may no longer match.

3. Custom Apps and Shopify Functions

Audit your app stack and log all your custom applications. Log details such as what the app does, its source code repository, hosting provider, external services it calls, technical owner, dependencies, etc. 

Shopify's current app tooling also includes configuration in the handover. Apps created through Shopify's Dev Dashboard, for example, can have versioned configurations covering URLs, API scopes and webhook API versions.

Also take inventory of any apps using Shopify Functions. Stores on any Shopify plan can use public App Store apps that contain Functions, while custom apps that use Shopify Function APIs require Shopify Plus. Some individual Function capabilities are also limited to Plus.

4. Webhooks, Scheduled Jobs and Background Processes

Webhooks may push orders to another system, a scheduled job might import inventory every night, a serverless function could update prices, and middleware may transform data between Shopify and an ERP. Document all of this. For each automated process, log:

• Trigger or schedule

• Source system

• Destination system

• Hosting environment

• Repository

• Authentication method

• Error-handling behaviour

• Retry logic

• Monitoring and alerts

• Responsible vendor or team

• Business impact if it fails

Shopify's webhookSubscriptions GraphQL query returns shop-scoped subscriptions created through the API for the current app and shop. It doesn’t return app-specific subscriptions configured in shopify.app.toml. Shopify recommends app-specific webhook subscriptions for most apps.

5. Ecommerce Integrations and Third-Party Vendors

Create an integration map showing everything connected to Shopify. Depending on your business, this could include an ERP, PIM, OMS, WMS, 3PL, POS, payment provider(s), marketing platform, loyalty program, subscription platform, marketplace connector, customer service software, etc.

For each, determine which system owns each data point and how often it moves. This way your new agency won’t accidentally break the operating model behind your storefront while working on other projects or fixes.  

6. Credentials, Domains and Infrastructure

Confirm merchant-controlled or appropriately shared administrative access to things like your domain registrar, DNS, Git provider, cloud hosting, content delivery services, databases, error monitoring, API platforms, Google Analytics 4, Google Tag Manager, Google Search Console. Google Merchant Center, Meta Business Manager, email and SMS platforms, design files, password or secrets management tools, and third-party app dashboards. 

Record where the credential is securely stored, what it controls, who owns it and who should have access. Once responsibility has moved to the new agency, rotate sensitive credentials where appropriate.

7. Analytics and Tracking

One aspect of an agency handover that shouldn’t be forgotten is taking a snapshot of your store’s analytics before any new projects, both to set new goals and to separate pre-existing problems from new ones. 

Record a baseline for metrics like sessions, conversion rate, revenue, average order value, organic traffic, and error rates. This gives the new agency something concrete to compare against after its first releases.

8. Open Bugs, Technical Debt and the Existing Backlog

If there’s any unfinished work floating around, the incoming agency needs to know about it. Build a list of any known bugs, intermittent issues, performance problems, deprecated APIs or dependencies, apps scheduled for replacement, work in QA and work waiting for deployment. 

This way, your new agency can get the whole picture regarding the scope of their partnership with you right away. They'll know what they’re inheriting so they can better plan fixes and improvements, and this information will also inform their planning phase as they tackle your to-dos. 

Who Owns Custom Shopify Code When an Agency Changes?

Ownership of custom Shopify code depends on the contract, statement of work, licences, and applicable intellectual-property law. That is why you should review all your agreements before ending an agency relationship. This could include agreements for theme development, custom apps, middleware, Shopify Functions, design files, proprietary agency frameworks, third-party libraries, and more. 

If the agreement assigns ownership of bespoke deliverables to the merchant after payment, confirm that all relevant source code and documentation have actually been delivered. Third-party components might be governed by separate licences, while an agency may also use proprietary tools that were never sold or assigned to the merchant. Get clarification on anything unclear before the outgoing agency disappears from the Slack channel!

What Should a Shopify Support Retainer Include?

Once everything has been audited, listed, and planned, the next step is agreeing on how ongoing Shopify maintenance services will operate. Your Shopify support retainer should define:

1. The Scope: What’s included. This could be bug fixes, theme maintenance, app troubleshooting, integration support, performance optimization, CRO work, platform updates, release support, etc.

2. Capacity: Clarify whether support is sold as a fixed number of monthly hours, reserved team capacity, a managed-services package, or a combination of maintenance and roadmap development. Ask what happens to unused capacity and what happens when demand exceeds the monthly allowance.

3. Support Hours: Clarify whether coverage applies only during business hours or includes evenings, weekends, and holidays, and whether emergencies can receive after-hours support. 

4. Response Targets: A response target defines how quickly the support team acknowledges and begins triaging an incident. Resolution is harder to guarantee because the root cause may sit with Shopify, an app vendor, a payment processor, an ERP provider, or another external system.

Example P1-P4 Ecommerce Support SLA Framework

While Shopify doesn’t define a universal P1-to-P4 severity framework for agency support, you can use this example support framework as a starting point when building your SLA. 

While this is a good place to start, you’ll need to consider your revenue exposure, operating hours, internal resources, and the support package you're purchasing.

Conclusion

A good Shopify agency transition preserves what works while giving the new team enough visibility to improve what doesn't. This means treating the handover as an operational and technical project, not an exchange of Shopify login information. Secure ownership, transfer access, audit the code, map the integrations, agree on the SLA and then start improving the store.

For merchants looking for a Shopify support agency to take over an existing store, Blue Badger can audit the current environment, identify technical and operational risks, establish a stabilization plan, and provide ongoing Shopify Plus support and maintenance after the transition. Get in touch with us today to learn more.