Chemical peels are widely used as therapeutic agents in dermatology and cosmetology. This study aims to explore the differences in the effectiveness of azelaic and pyruvic acid peels in the treatment of acne vulgaris. Eligibility criteria for participants were: female gender, 18-25 years of age, no dermatological treatment within the last 12 months and mild to moderate papulopustular acne. We treated 120 young women (with a mean age of 22 years old) with six peeling sessions at 2-week intervals. In the parallel clinical study design, one randomized group (n = 60, 50%) was treated using azelaic acid (AA), whereas the second group participated in pyruvic acid (PA) sessions. We evaluated the patients clinically twice (before and after treatment), using the Scale of Hellegren-Vincent Severity Symptoms to assess the acne diagnosis, and the Nati Analyzer to estimate the skin properties (oily skin, desquamation, porosity, and moisture). The clinical evaluation of the patients demonstrated a significant reduction of acne severity symptoms in both the AA and PA groups, after the peeling sessions. An effect was also found in terms of decreasing desquamation and the oiliness of the skin. PA showed a more significant reduction of greasy skin than AA. In conclusion, after the six peeling sessions using AA and PA, all patients showed better skin parameters in term of reduced oiliness and desquamation. Both AA and PA peelings are a safe and efficient treatment for mild acne, however, during the selection of one of the two acids, side effects, skin properties, and patients' preferences should be taken into account. This study was registered in the ISRCTN registry (registration number ISRCTN79716614, 17/01/2020).