Quick question... is it safe to store things in the Arch Mage's quarters once you become the head of the college?

Yep, I store things in all of the wardrobes, the big chest, the safe, and occasionally even the buckets.

Thanks for the quick reply !

One thing to remember is if you come back within a couple weeks almost all containers might seem safe but might not be. I'm not contradicting Hungry Donner though. I don't have a house yet (though I am Arch Mage) and I've been using a barrel in the room given to me in the College of Winterhold when I first applied there. All of the other cubbies/rooms in that area seem marked owned, presumably by the students/faculty that live there, so I'm thinking it's safe but I'm not sure. Now that I think of it, it might be possible to use the console to check ownership, but if so I can't find out how.

The Arch Mage room storage stuff is 100% safe. Ive been using it it since I was like lvl 10, im now lvl 50, but recently bought a house in Markarth so ive been transporting stuff to that one.

yeah its safe, also the first room they give you is safe too, although i do think it reset on me once early in the game but it was fine after that..containers are tricky..there are other safe containers in the game besides houses you buy..the arch mage room respawns every so often which is cool..i live in markarth...thats where all my stuff is...but i'm thane of white run and riften also and own the riften house as well but don't store stuff there since markarth is way cool...whiterun house svcks, the town is cool but the house is not my style...arch mage room is perfect actually, its kinda better when you don't live there though cause that way you can go back every so often to collect soul gems and other stuff that respawns.

I am now playing mage but she joined the thieves guild because she is cloak and dagger political type. I like the chests in ragge flagon. I have bed, use 3 containers, and have quick access to a vendor. Not sure if my character will do tg quest line . Ooc she should but she just wants to learn from thieves an have contacts not really get deep into guild.