Customizing Shopify email notifications after WooCommerce migration (2026)

After migrating from WooCommerce to Shopify, your automated email notifications need attention. Your WooCommerce emails (using WooCommerce Email Customizer, MailPoet, or Klaviyo for WooCommerce) won't carry over — Shopify uses its own notification system. Here's how to set up Shopify's transactional emails to match or improve on your WooCommerce setup.

WooCommerce emails vs Shopify notifications: key differences

Email type	WooCommerce	Shopify
Order confirmation	New Order (to customer)	Order confirmation
Order shipped	Completed Order email	Shipping confirmation (sent when tracking added)
Order refunded	Refunded Order	Refund notification
Order cancelled	Cancelled Order	Order cancelled
Abandoned cart	Plugin required	Built-in abandoned checkout (1 email)
Account creation	Customer New Account	Customer account welcome
Password reset	Customer Reset Password	Customer account password reset
Invoice / receipt	Processing Order email	Not separate — order confirmation serves as receipt
Backordered items	Backorder notification	No equivalent — handle via custom app or Klaviyo
Staff new order alert	New Order (to admin)	New order notification to staff

Shopify notification system overview

All Shopify notifications are managed in Settings → Notifications. Each notification has:

• An HTML email template (editable)
• A plain text version (auto-generated or customizable)
• A Liquid template engine for dynamic content (order details, customer name, etc.)
• On/off toggle

Shopify notifications use the Liquid templating language — the same templating used in Shopify themes. This is more powerful than WooCommerce's shortcode-based email system but requires familiarity with Liquid syntax for significant customizations.

Step 1: Set your sender email address

Before customizing templates, set your from address:

1. Shopify Admin → Settings → Notifications → Sender email
2. Enter your business email (e.g., orders@yourdomain.com)
3. Verify the email address (Shopify sends a verification link)
4. For best deliverability: verify your domain's SPF and DKIM records in Settings → Domains → Email authentication

Default sender: If you don't verify a custom email, Shopify sends from a @shopify.com address, which looks unprofessional and may have lower deliverability.

Step 2: Add your email header and branding

Shopify has a global email header/footer template:

1. Settings → Notifications → Email templates (at the bottom)
2. Edit your store logo, accent color, and basic layout
3. This applies to all Shopify notification emails

The default Shopify email template is clean and modern — for most stores, the global template customization (logo + color) is sufficient without touching individual templates.

Step 3: Customize individual notification templates

Order confirmation

The most important email. Customers read order confirmations — they check the order is correct and use it as their receipt.

WooCommerce → Shopify differences to verify:

• Your business name and address appear correctly
• All line items, quantities, and prices display correctly
• Shipping address and method displayed
• Payment method shown (for customer reference)
• Any custom text you had in WooCommerce (e.g., "Thank you for ordering! Returns accepted within 30 days.") — add this as custom content in the template

To add custom text to order confirmation in Shopify, find the appropriate section in the Liquid template and add HTML content. Example adding a message above the order summary:

{% raw %}{% if order %}
<p style="color: #666; font-size: 14px; margin: 0 0 20px;">
  Thank you for your order. We'll send shipping confirmation when your package is on its way.
  Questions? Email us at support@yourstore.com
</p>
{% endif %}{% endraw %}

Shipping confirmation

In WooCommerce, the "Completed" status triggers the shipping email. In Shopify, the shipping confirmation email is sent when you add a tracking number to the fulfillment.

Key settings:

• Settings → Notifications → Shipping confirmation: verify enabled
• The email includes a tracking link automatically when a tracking number is added
• Customize the "Out for delivery" and "Delivered" notifications if your carrier supports these events

Abandoned cart email

Settings → Notifications → Abandoned checkout: the single-email native abandoned cart. Timing: 1 hour (default) or 10 hours.

For a multi-email sequence, use Klaviyo or Shopify Email instead (see abandoned cart migration guide). Disable Shopify's native abandoned cart email if using Klaviyo to avoid duplicate sends.

Using Klaviyo for transactional emails

If you used Klaviyo on WooCommerce for transactional emails (many stores route order confirmation through Klaviyo for better analytics and design control), Klaviyo can handle transactional emails on Shopify too.

After connecting Klaviyo to Shopify:

• Klaviyo receives Shopify webhook events: Order Placed, Order Fulfilled, Refund Issued, etc.
• You can build Klaviyo flows triggered by these events
• Disable the equivalent Shopify notification to avoid sending both

Klaviyo transactional email flows offer:

• Better analytics (open rates, click tracking per email)
• A/B testing on order confirmation messaging
• Dynamic product recommendations in shipping confirmation ("You might also like...")
• Consistent design across all emails (transactional + marketing)

Email design: matching your WooCommerce branding

WooCommerce Email Customizer plugins (like YITH WooCommerce Email Templates or Email Customizer Plus) allowed pixel-level email design control. Shopify's built-in customization is less flexible.

Options for more control over Shopify email design:

• Edit Shopify notification HTML directly: Full Liquid + HTML editing available in Settings → Notifications → individual template. Requires HTML/CSS knowledge.
• Klaviyo: Drag-and-drop email builder with full design control, including transactional emails.
• Omnisend: Alternative to Klaviyo with email builder for transactional + marketing emails.
• Email Customizer apps: Apps like "Email Template by T-Email" or "Orderly Emails" provide visual editors for Shopify notifications without coding.

Staff notification setup

WooCommerce sent new order notifications to the admin email. Shopify does the same:

1. Settings → Notifications → Orders section → New order
2. Add recipient email addresses (comma-separated for multiple staff)
3. Toggle on/off per notification type

For stores with different departments receiving different notifications:

• Fulfillment team: receives new order notifications
• Support team: receives refund requests and cancelled orders
• Finance: receives risk-flagged orders

Testing all notification emails

Before launch, test every notification email by triggering the event manually:

• Order confirmation: Settings → Notifications → Order confirmation → Send test email (or place a test order with test payment mode)
• Shipping confirmation: Create a test order, fulfill it with a tracking number, verify email received
• Abandoned cart: Start checkout on your store, don't complete, wait for timing to trigger (or use Klaviyo's preview)
• Account creation: Create a test customer account

Check each email on mobile — most Shopify notification emails are mobile-responsive by default, but verify custom HTML additions don't break mobile layout.

Email notification migration checklist

• Verify sender email address is set to your business domain
• Configure domain authentication (SPF/DKIM) in Settings → Domains
• Add your logo and brand color to the global email template
• Customize order confirmation with any custom messaging from WooCommerce
• Verify shipping confirmation email includes tracking link
• Set up abandoned cart email (native 1-email or Klaviyo multi-email sequence)
• Disable Shopify native notifications where Klaviyo handles them instead
• Configure staff notification recipients for new orders, refunds, and cancellations
• Send test emails for every notification type
• Check email renders correctly on mobile and in Gmail, Outlook, Apple Mail

Email notifications are often the last thing stores configure before launch, but they're the first thing customers interact with after purchasing. Get them right — a poorly branded or incorrect order confirmation email is a trust signal that your migration didn't go smoothly.