I think the concern really is that you don't want your skin to dry up in the area where you're applying the acne treatment. It will depend on your skin type and whether your skin tends towards oily or dry, but in my case if I put my moisturizer on top then there's already a significant barrier to my pores in the form of the acne treatment, kinda blocking it from fully moisturizing my skin in that area. Whereas, when I apply the acne treatment on top, the benzoyl peroxide is still effective at breaking down the acne causing bacteria without drying out your skin as much? I can only apply it once a day. If I do it twice, my skin dries out. For the occasional white heads I get, putting it on last has been quite effective.