7.13.6   What can I do if my Spam or Junk mailbox in Apple Mail disappeared?

First, from Mail’s View menu, choose Show Sidebar (or Show Mailbox List on older versions of macOS) if necessary so that the mailboxes are visible.

Junk Mailbox

If you’re using the recommended setup described in Switching From the Spam Mailbox to the Junk Mailbox, the special Junk mailbox should always be visible within each account. To see the spam messages from all accounts consolidated into a single All Junk mailbox, you can click the + button next to Favorites at the top of Mail’s mailbox list and then add the All Junk mailbox to the favorites.

Spam Mailbox

If you are instead using a Spam mailbox under On My Mac, it is most likely it’s still there but Mail is currently hiding it. To show the Spam mailbox:

1. Locate the On My Mac section of the mailbox list. It is typically below the Mailboxes and Smart Mailboxes sections of the mailbox list. You may need to scroll down in order to find this. (macOS may have made the scroll bars invisible, but you can scroll down by two-finger dragging on your Mac’s trackpad or by using the scroll ball on the mouse.)
2. Move your mouse over On My Mac in the mailbox list. Then click the > or Show button that becomes visible at the right.