How to Delete Messages in iOS Mail From Notification Center

To move a message to the Trash folder from an iOS Mail alert in the Notification Center:

Select an email alert in the Notification Center to open an options menu. Choose Archive or Delete (depending on the phone settings) to remove the email from the Inbox. The message will move accordingly.

How to Delete Mail in iOS Mail From a Banner

If your Mail notifications are set to include banners (alerts that show up at the top of the screen) when you get a new message and the iPhone is unlocked, you can also delete and archive messages.

Either press (with 3D Touch) or swipe down (if the phone doesn’t have 3D Touch), then choose Delete or Archive.