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How to migrate Shopify stores to Patient Copilot

Migrating from Shopify to Patient Copilot helps you bring your ecommerce data, customer records, order history, and marketing workflows into one platform. This guide explains how to prepare your Shopify store, connect Shopify to Patient Copilot, import supported data, configure future sync settings, rebuild key automations, and validate your migration before fully transitioning. Patient Copilot’s Shopify integration supports importing and syncing products, collections, contacts, orders, and transactions. It also supports future ecommerce automation using triggers such as Order Submitted and Payment Received. ## Note: Changes to Shopify connection setup Shopify is updating how new integrations connect to third-party apps and moving to an OAuth-based setup. Here’s what this means for you: 1. Already connected your Shopify store to Patient Copilot: No action needed. Your integration will continue to work as-is. 2. Your Shopify store has custom app creation flow: You can continue using the steps below to connect. 3. New Shopify store without the custom app option: Shopify no longer shows this option on some newer stores (specifically from Jan 1, 2026). Our updated OAuth-based connection flow is coming soon and will make setup easier for you. What’s coming: We’re rolling out a new OAuth-based Shopify connection which is more secure, faster to set up, and aligned with the Shopify’s latest standards. It will be available soon and this guide will be updated the moment it goes live. * * * ## What is the Shopify to Patient Copilot Migration? The Shopify to Patient Copilot migration allows store owners to move supported ecommerce data from Shopify into Patient Copilot so they can manage contacts, products, orders, payments, and follow-up automation in one place. The migration uses the Shopify integration in Patient Copilot to import historical data and keep selected data synced going forward. This migration is best used when you want to centralize ecommerce operations, customer communication, and sales automation inside Patient Copilot. Some parts of the migration are handled through the native Shopify integration, while other items, such as workflows, store pages, payment settings, and team processes, should be reviewed and rebuilt manually. * * * ## Key Benefits of Migrating Shopify to Patient Copilot Migrating your Shopify store to Patient Copilot helps reduce platform switching and gives your team a more complete view of ecommerce activity, contacts, and automation opportunities. - Centralized ecommerce data: Import supported Shopify products, collections, contacts, orders, and transactions into Patient Copilot.

  • Improved customer follow-up: Use ecommerce data with Patient Copilot CRM tools to create better customer communication and segmentation.
  • Automation-ready order activity: Use triggers such as Order Submitted and Payment Received for workflow automation after the Shopify integration is connected.
  • Simplified migration planning: Review Shopify data, workflows, payments, and store operations before transitioning fully to Patient Copilot.
  • Ongoing sync control: Choose which supported Shopify data should continue syncing into Patient Copilot after the initial import. * * * ## Before You Begin A successful migration starts with the right access, permissions, and expectations. Reviewing these requirements before setup helps prevent missing data, failed imports, and sync limitations. Before migrating, make sure you have: - Admin access to the Shopify store
  • Admin access to the Patient Copilot sub-account
  • Permission to create or manage custom apps in Shopify
  • Access to generate a Shopify Admin API access token
  • The Shopify store URL or store name
  • A clear list of automations, notifications, checkout flows, and customer follow-up processes that need to be rebuilt in Patient Copilot Important Shopify plan limitation: Shopify Basic may not provide access to customer PII through the updated Shopify API. This can prevent contacts, orders, and transactions from syncing into Patient Copilot. Products and collections can still be imported and synced on Shopify Basic, but contacts, orders, and transactions may require Shopify Grow, Advanced, or Plus. If your Shopify plan does not provide access to the required customer or order data, some import or sync options may appear unavailable during setup. * * * ## What Shopify Data Can Be Imported and Synced? The Shopify integration includes two important migration choices: one-time historical import and future sync. Understanding the difference helps you decide what data to bring into Patient Copilot now and what data should continue updating after the connection is complete. | One-Time Import Options | Future Sync Options | | --- | --- | | Contacts | Contacts | | Orders | Orders | | Transactions | Transactions | | Products | Products | | Collections | Collections | | | Order Submitted trigger | | | Payment Received trigger | Note: Contact import includes Shopify customers who have placed an order in the past. Customers who have not placed an order may not be included in the Shopify contact import. The import and sync process may take time to complete depending on the size of the Shopify store and the selected data types. * * * ## Create a Custom App in Shopify Before we setup integration we need to create a custom app in your Shopify store. 1. Log in to your Shopify store and click Apps from your Shopify dashboard.!(https://assets.patientcopilot.ai/4f743c1d61dca0ec.png) 2. Click Develop apps at the top of the screen.!(https://assets.patientcopilot.ai/b35fbf3f9abcd083.png) 3. Click Allow custom app development. Note: If custom app development is already enabled, Shopify will take you directly to the app creation screen.!(https://assets.patientcopilot.ai/12ac585d1ffc1818.png) 4. On the next screen, click Allow custom app development again to confirm.!(https://assets.patientcopilot.ai/798b2ac19e191c60.png) 5. Click on Create an app!(https://assets.patientcopilot.ai/dc28d85c28415d21.png) 6. Enter a name for the App (for example “Marvel’s App”), select your email under App developer and click on Create App!(https://assets.patientcopilot.ai/89f2f91aebc72cc7.png) 7. Click Configure Admin API scopes to set up the required Admin API permissions.!(https://assets.patientcopilot.ai/eaa586308a6c14c0.png) 8. Search or scroll to Orders, then enable at least the read_orders permission.!(https://assets.patientcopilot.ai/637f98a306638167.jpg) 9. Add the read_customers scope. In configuration edit the Admin API Integrations. In this section under customers, select the read_customers tick box.!(https://assets.patientcopilot.ai/2f882617bfe9bff3.png)!(https://assets.patientcopilot.ai/27cfe46489956685.png) 10. Search or scroll to Products, then enable at least the read_products permission.!(https://assets.patientcopilot.ai/7c30577ed04760d4.png) 11. After enabling read access for Orders, Customers, and Products, click Save in the top-right corner.!(https://assets.patientcopilot.ai/b2210e14c1dbaf5e.png) 12. After saving the app, click Install app.!(https://assets.patientcopilot.ai/673e31bed5d6de52.png) 13. In the confirmation pop-up, click Install.!(https://assets.patientcopilot.ai/cbb164c4c79f35bf.png) 14. After the app is installed, go to the API credentials section and click Reveal token once to view the Admin API access token required for the Shopify integration. Important: Shopify may only show this token once. Copy and store it securely before leaving the page.!(https://assets.patientcopilot.ai/f8174a5bb99b9c5d.png) 15. Copy the Admin API access token by clicking the clipboard icon.!(https://assets.patientcopilot.ai/bc71e0292947cf10.png) * * * ## Connect Shopify to Patient Copilot Connecting Shopify to Patient Copilot starts the migration setup process. This is where you enter the Shopify store details, choose which historical data to import, and select what should continue syncing in the future. 1. Open the Patient Copilot sub-account and Go to Settings > Integrations > Shopify. Click Connect.!(https://assets.patientcopilot.ai/a4b98fab860f8f0e.png) 2. Enter the Shopify store URL or store name and Paste the Shopify Admin API access token.!(https://assets.patientcopilot.ai/eacd96c7c070488d.png) 3. Continue to the import selection screen. Select the Shopify data you want to import: - Contacts - Orders - Transactions - Products - Collections!(https://assets.patientcopilot.ai/09e141da81fc186f.jpg) 4. Continue to the sync settings screen. Select the Shopify data and events you want to sync going forward: - Contacts - Orders - Transactions - Products - Collections - Order Submitted trigger - Payment Received trigger!(https://assets.patientcopilot.ai/1d04d2c9e1dc66a4.jpg) 5. Click Save. Tip: For a full Shopify store migration, select all available import and sync options unless your migration plan requires only specific data types. This helps ensure supported historical data is imported and future Shopify activity continues syncing into Patient Copilot. * * * ## Review Imported Products and Collections Products and collections are core parts of the Shopify migration because they determine how your ecommerce catalog is organized in Patient Copilot. Reviewing imported catalog data helps ensure your store setup, checkout flow, and customer experience are accurate before going live. After the import completes: - Review imported products under Payments > Products > Products.
  • Review imported collections under Payments > Products > Product Collections.
  • Confirm product names, descriptions, images, prices, and inventory details.
  • Confirm products are assigned to the expected collections.
  • Check whether SEO fields imported as expected.
  • Update any product or collection details that require manual cleanup. Important product and collection notes: - Taxes are not mapped to products while importing or syncing products.
  • If Shopify SEO details are still using default settings and have not been changed, the SEO data may be received as null in Patient Copilot. Product imported from Shopify to Patient Copilot:imageimage Collections imported from Shopify to Patient Copilot:imageimage * * * ## Rebuild Ecommerce Operations and Automations in Patient Copilot The Shopify integration helps move supported data, but some business operations still need to be recreated or reviewed manually in Patient Copilot. Rebuilding these items ensures your team can continue selling, communicating, and following up after the migration. | Area to Review | What to Rebuild or Confirm | | --- | --- | | Ecommerce store pages | Confirm your store pages are created and organized in Patient Copilot. | | Checkout pages | Rebuild checkout pages and confirm the purchase flow works as expected. | | Thank-you pages | Create or update post-purchase thank-you pages. | | Payment gateway settings | Connect and verify payment processing settings in Patient Copilot. | | Shipping and delivery settings | Recreate shipping, delivery, or fulfillment-related settings as needed. | | Order confirmation communication | Rebuild emails, SMS messages, or notifications sent after purchase. | | Abandoned checkout recovery | Configure abandoned checkout follow-up to recover missed sales. | | Customer follow-up workflows | Recreate post-purchase, win-back, review request, or upsell workflows. | | Internal notifications | Set up team alerts for new orders, payments, or fulfillment tasks. | | Tags, segments, and customer lists | Recreate customer organization rules for segmentation and reporting. | | Invoices, documents, and templates | Rebuild reusable templates needed for customer or internal processes. | | Team SOPs and operational processes | Update internal documentation so your team knows how to manage ecommerce operations in Patient Copilot. | For ecommerce workflows, go to Automations > Workflows and recreate the Shopify workflows you still need in Patient Copilot. Use ecommerce triggers such as Order Submitted and Payment Received where applicable. Use the following resources to rebuild key ecommerce operations in Patient Copilot: - How to Set Up an E-Commerce Online Store Websites Use this article to set up your Patient Copilot ecommerce store, including store pages, checkout pages, thank-you pages, products, order tracking, and fulfillment settings.
  • Recover Lost Sales with Automatic Abandoned Checkout Emails Use this article to configure abandoned checkout emails and recover customers who leave before completing their purchase.
  • Manual Payment Method in E-commerce Stores & Order Forms Use this article if your ecommerce process includes manual payment options, offline payments, or orders that need to be marked as paid manually. * * * ## Manage Sync Settings After Migration After Shopify is connected, sync settings can be adjusted to control which supported Shopify data continues updating in Patient Copilot. Managing these settings helps keep your Patient Copilot account aligned with Shopify during the transition period. After the integration is connected: - Return to Settings > Integrations > Shopify.
  • Review the enabled sync elements.
  • Enable or disable future sync options based on your migration plan.
  • Monitor imported records for accuracy.
  • Review workflow behavior after new synced Shopify activity appears in Patient Copilot. To reimport missed data, disconnect and reconnect the Shopify integration, then select the data you want to import again. Review records carefully after reimporting to confirm the expected data was added or updated. * * * ## Decommission Shopify After Validation Decommissioning Shopify should happen only after your team confirms that data, checkout operations, customer communication, and internal processes are working correctly in Patient Copilot. A careful shutdown prevents lost records, interrupted sales, and missed customer follow-up. Before canceling Shopify: - Complete a final export of Shopify products, customers, and orders.
  • Confirm critical data exists in Patient Copilot.
  • Confirm Patient Copilot checkout, payments, shipping, and notifications are configured.
  • Confirm workflows and follow-up automations have been tested.
  • Train team members on the new Patient Copilot process.
  • Save SOPs and migration notes for future reference.
  • Cancel Shopify only after your team is confident the migration is complete. * * * ## Frequently Asked Questions Q: Which Shopify customers are imported as contacts? A: Contact import includes Shopify customers who have placed an order in the past. Customers who have not placed an order may not be included in the Shopify contact import. Q: Can I choose only certain Shopify data to import? Yes. During setup, you can select which supported data types to import, including contacts, orders, transactions, products, and collections. For a full store migration, select all available import and sync options unless your migration plan requires only specific data types. Q: What is the difference between import and sync? Import brings selected existing Shopify data into Patient Copilot during setup. Sync controls which supported Shopify data and events continue updating in Patient Copilot after the connection is saved. Q: Where can I confirm that my Shopify products and collections imported successfully? Review imported products under Payments > Products > Products and imported collections under Payments > Products > Product Collections. Q: Are Shopify taxes imported with products? Taxes are not mapped to products during Shopify product import or sync. Q: How are Shopify order statuses handled in Patient Copilot? Synced Shopify order statuses are marked as either Completed or Cancelled in Patient Copilot. Q: Does Patient Copilot create multiple transactions for a Shopify order? No. Patient Copilot creates one transaction for each synced Shopify order. Q: Why aren’t my contacts syncing from Shopify? Shopify Basic may no longer provide access to customer PII through Shopify’s updated Admin API. Customer PII includes details such as customer names, email addresses, phone numbers, and addresses. Patient Copilot needs this information to create or update contacts. Note: To sync Shopify contacts into Patient Copilot, you may need to upgrade to Shopify Grow, Advanced, or Plus. Q: What Shopify data can sync on the Basic plan? On Shopify Basic, you can still import and sync: - Products
  • Collections You may not be able to sync: - Contacts
  • Orders
  • Transactions This is because contacts, orders, and transactions rely on customer PII, which may not be available through Shopify’s updated API on the Basic plan. Q: It used to work before. Why did my Shopify contact, order, or transaction sync stop working? Shopify updated its API access rules, and the older Shopify API version that previously allowed customer PII access on all plans is being deprecated. As Patient Copilot moves to Shopify’s updated API, these Shopify plan-based restrictions may apply. This can affect both Admin API access and webhook data. If Shopify does not return customer data through the API or webhook event, Patient Copilot cannot create the related contact, order, or transaction record. Q: Where can I check or manage Shopify app permissions? You can manage app permissions from your Shopify admin. Read here for more details. Q: Where can I find my Shopify store name? Log in to your Shopify admin and look at the URL in your browser. Your store name is the value that appears after /store/ in the Shopify admin URL. For example, if the URL contains: admin.shopify.com/store/ef760-ef Then the Shopify store name is: ef760-ef !(https://assets.patientcopilot.ai/27416098811fc0d8.png) * * * ## Related Articles - How to migrate Shopify stores to Patient Copilot, including products, collections, orders, contacts, and transactions
  • Shopify to Patient Copilot Migration Guide
  • How To Integrate Shopify With Patient Copilot
  • How to Set Up an E-Commerce Online Store Websites
  • Recover Lost Sales with Automatic Abandoned Checkout Emails
  • Manual Payment Method in E-commerce Stores & Order Forms