If you added an email tool to your store, two confirmation emails for one order can mean the platform and the tool are both reacting to the same order. Adding the tool doesn't switch off the platform's emails. Omnisend, for example, says plainly that it doesn't disable Shopify's notifications for you. The fix is to decide one sender for each order email, but on standard Shopify plans the order confirmation itself can't be switched off, only shortened.

Customers notice: two designs, two subject lines, and a reasonable question about whether they've been charged twice.

Find out which two systems are sending

Don't switch anything off until you know where each email comes from. Place a test order with your own address and keep both emails.

Compare the emails. Look at the sender name and address, the subject line and the design. Shopify's notifications use the templates in your Shopify notification settings; an email tool uses the designs you built in it. Note the time each one arrived, too. On Shopify, the order confirmation goes out when the order is placed. Omnisend's order confirmation workflow is triggered when the order is marked as paid, so if payment is captured after the order is placed, its email arrives later, and Omnisend says orders whose status changes more than three hours after placement don't trigger the workflow at all.

Check the sender details. In Gmail, a "via" label with a website name next to the sender appears when the message was sent through a domain other than the one in the From address. It doesn't always show, but when it does, the domain can point to the service that sent the email.

Check each system's own records. In Omnisend, each automation has a report that shows emails sent, with an activity feed per send. If your test order appears in an Order Confirmation workflow there, that's one sender.

Don't assume it's two different systems. Omnisend warns that if you build a confirmation workflow for one product category, you need to adjust your standard workflow so the same order doesn't get two confirmations. Review apps, order-tracking apps and other email tools can also send order emails. If neither Shopify nor your email tool explains the second email, go through your installed apps.

Map every order email to one sender

Do this for every email a customer can get about an order, not just the confirmation. Here's how it looks for Shopify plus Omnisend:

Email Shopify sends Omnisend can send Switching off Shopify's version
Order confirmation When the order is placed Preset workflow, triggered when the order is paid Not on standard plans; shorten it instead
Shipping confirmation When you fulfil the order Preset workflow, triggered when the order is fulfilled See the shipping section below
Out for delivery, Delivered From carrier tracking events Only with a tracking app that sends these events to Omnisend Can be switched off in notification settings
Order canceled, Order refund When you cancel or refund Order Canceled preset; refunds need a custom workflow Per order, when you cancel or refund
Abandoned checkout If switched on Preset workflow Yes
Account emails (password reset, invite) Always No Shopify only; you can restyle them

Fill in your own version with a third column: who sends it after the change. Every row should have exactly one name in it.

Order confirmations and order updates aren't marketing

Order confirmations and shipping updates are transactional: they're about something the customer just did. Omnisend's order and shipping confirmation workflows are triggered regardless of the contact's subscription status, so a customer who didn't tick the newsletter box still gets them.

That matters when you move these emails out of Shopify. If you rebuild an order email as a campaign or in a workflow that only reaches subscribers, the customers who didn't opt in will stop getting it. Use the transactional workflow types for order emails, and keep the content about the order.

Switch over in this order

  1. Build and publish the new workflow first. Omnisend notes that unpublished workflows send nothing, and that its workflows don't send for orders placed before they went live.
  2. Place a test order and check that the new email arrives with the right order number, items, totals and addresses.
  3. Only then switch off or shorten the Shopify version. Omnisend's own advice is the same: enable and test the workflow before disabling the Shopify notification.
  4. Place a second test order and confirm each email now arrives once.

Doing it the other way round can leave a gap where customers get no confirmation at all.

The order confirmation you can't switch off

Shopify's help says most customer notifications are sent automatically and can't be deactivated, and order confirmation isn't in its list of ones you can. Omnisend's guidance for standard Shopify plans is to replace the content of Shopify's order confirmation with a short thank-you message and send the full order details from Omnisend.

A short version that still does its job:

  • the order number;
  • one line saying a full confirmation with the details follows by email;
  • your contact address.

Keep the order number. If the Omnisend email is delayed or filtered, the customer still has proof the order went through.

On Shopify Plus the two help centres differ: Shopify's help says the store owner can contact Shopify Support to turn off specific notifications, while Omnisend's guide says Plus stores can disable them in Shopify's notification settings. Check your admin first, and ask Shopify Support if the option isn't there.

Shipping confirmation: check what your admin offers

The two help centres describe this differently. Omnisend tells Shopify stores to disable the Shipping confirmation notification in Shopify's notification settings, and notes that only notifications with a toggle there can be switched off. Shopify's help describes switching off the shipping confirmation per order: when you fulfil an order, you deselect the option to send shipment details to the customer.

So open your notification settings and look. If Shipping confirmation has a toggle, use it once the Omnisend workflow is live. If it doesn't, you'd have to untick the option on every fulfilment, which is easy to forget. In that case it may be simpler to keep Shopify's shipping confirmation and not build one in Omnisend at all.

Abandoned checkout emails

These are marketing reminders, not order emails, but they duplicate in the same way. If you send cart reminders from an email tool, switch off Shopify's own abandoned checkout email; Omnisend's instructions point to the abandoned checkout option in Shopify's checkout settings. What those reminders should say is covered in how to recover abandoned carts.

Do you need a second system for order emails at all?

If the only reason for moving order emails was design, you may not need to. You can edit Shopify's notification templates directly, and Omnisend even shows how to export an email design from its builder as HTML and paste it into a Shopify notification, which keeps Shopify as the only sender.

Moving the emails to Omnisend makes sense when you want them in the same place as your other automations: a shipping confirmation that changes by delivery country, or an order confirmation that differs by order value. Its order and shipping confirmation workflows are available on all Omnisend plans. The limit to plan around is the one above: on a standard Shopify plan, Shopify's short confirmation still goes out, so customers will always get two emails about a new order. The aim is to make them clearly different — a short receipt and a full confirmation — rather than two copies of the same thing.

Test order checklist

After any change, place one test order and check:

  • one order confirmation with full details, plus Shopify's short version if you're on a standard plan;
  • nothing arrives from a third system you forgot about;
  • the totals, discount and shipping line match the order in Shopify;
  • after you fulfil it, one shipping confirmation with a working tracking link (Omnisend notes the button is empty if no tracking URL reaches it);
  • a customer who isn't subscribed to marketing still gets every order email.