My iCloud storage is full but I have over 45 GB free

I just spoke with Apple support. The e-mail we received appears to be a phishing scheme not sent by Apple. I am forwarding it to the fraud department.

I get the same thing. I add a few ePubs that I have purchased from the publisher (Baen, O'Reilly, Manning, others), and iBooks insists that my iCloud storage is full, even though I've upgraded to the 50GB tier and have 44GB free. It's like as soon as iBooks sees that you're over 5 GB, it just gives up and goes stupid.

I think I've found a solution, but it's painful. I signed out of iCloud on my MacBook Pro (which involved deleting data from my MBP). I then signed back into iCloud on my MBP. After a significant amount of time for iCloud to re-download data to my MBP, iBooks seems to be working correctly.

I still had to delete all of my books that were listed as zero bytes, and then re-add them from source, but this time iBooks was able to successfully upload them and I can now see them on my various iDevices.

I think that there is a bug in 10.11.4's support for iBooks/iCloud -- but it's possible that this is a remnant of the public beta (since I first connected iBooks to iCloud and upgraded my storage while still using the public beta and before iOS 9.3 was available.

I have talked to Apple Support, who suggested to boot my iMac in safe mode.

Once in Safe Mode, I've started iBooks and message was gone.

Restarted and back in "normal" mode, all good.

I guess the Safe Mode suggestion worked in my case, hope it stays that way.

Dod you actually read the post you replied to?

The email was NOT Apple, you need to read

Same problem here. My fix was just temporarily disabling WLAN and restarting iBooks. Then it worked fine.

This worked for me! Anyone else who has the issue addressed above should try this solution before deleting/restarting anything

Same thing happened to me on my iPhone. The issue resolved itself after I rebooted the phone.

It's a bug in iBooks' error reporting.

It appears that if iBooks on the Mac encounters a network or iCloud-related error for which it does not have error handling correctly built-in (e.g. it times out or the connection is dropped), it defaults to the misleading "Your iCloud storage is full" message.

See https://discussions.apple.com/thread/7603398?answerId=30579377022#30579377022 for a little more info.

I have submitted a bug report to Apple citing this thread (among others), so if you have any more details on the circumstances under which you encounter this error and can post them here, that might help.

Note also that you should not need to boot your Mac into safe mode or anything of that nature to resolve the error. It's network-related. When whatever network error iBooks encounters is resolved, syncing your books and PDFs to iCloud will resume. i.e. Unless you have deeper network problems, this will usually take care of itself.