Side Effects of Acne Medications. Over the years many side effects have been seen from prescription acne medicines. Acne medicines often contain very harsh chemicals that can be drying, irritating and cause staining of clothes and fabrics such as with benzoyl peroxide. For these reasons many people have turned to natural acne treatment methods in order to clear their skin. This has resulted in many people achieving clear skin by looking at their diet and other natural regimens.