iCloud Email Storage won't delete

Ignore what I said, I didn't read what you wrote properly.

Try opening mail preferences > accounts > mailbox behaviors and unchecking 'Store sent messages...' and 'store deleted messages' or changing the 'permanently erase...' option and then changing it back.

I had this same problem and I just found out the solution that worked for myslef. If you have a mac with the mail aplication open it up and go into the mail prefferences. Once there go to the accounts tab. Select your iCloud email adress. Then there are three tabs available. Select mailbox behaviors. Then down where it says trash uncheck the box that says "Store deleted messages on the server" and you can also select to permanently erase the deleted messages at different time incriments to prevent this problem from coming up in the future. My free space opened up right after I saved the preferences.

I hope this helps

How about using Iphone 6 Plus ? I got the same problem here. Even my email folder is empty, still i can see my storage using 2,5GB. My icloud storage has no contact, no email, no document, nothing at all. Even i had checked trash, draft, junk folder, its nothing there. But if you go to Setting, there is 2,5GB of used storage.

For the avoidance of doubt, have you tried deleting it from System Preferences.

Delete it (sign out) from iCloud, not Mail, Calendars and Contacts.

System Preferences>iCloud.

Go to www.icloud.com, login and delete the mail from the web interface

It's possible that your Mac was off, or Mail was not running during the original download of mail to it. On reconnection it would pickup where it left off.

My guess is that deleting your account from mail had the same effect as toggling the boxes and settings I mentioned.

Try checking your sent folder. I had the same issue and I had 2 gb's of mail in my sent folder, delete those and then empty your trash and that should solve your iCloud storage problems!