In my experience, cystic acne was related to my diet. I ate healthy as well, or so I thought. Sugar and dairy were the biggest culprits for me, and if you start reading ingredients you'll be amazed where you find sugar. A jar of planters peanuts for example contain sugar! Anyway, there may be sugar in the protein powder as well. Remember sugar is also referred to as high fructose corn syrup, fructose, corn syrup, glucose, etc.
I'm 33 years old and had mild acne as a teenager and moderate acne through my 20's. Finally I did a food illimination expiriment and discovered it was sugar, haven't had acne in 2 years. I also use dessert essence tea tree soap (from Amazon) and use jojoba oil or pure shea butter to moisturizer when needed. I recently read argan oil worked better but I haven't tried it yet. I think cystic acne is an indication your body is trying to purge toxins vs black or white heads which likely indicate clogged pores.