Aloe vera skin (AVS) is a major by-product of Aloe processing plants all over the world. In this study, response surface methodology was used to optimize microwave-assisted extraction (MAE) of bioactive compounds from AVS. The influence of extraction parameters, such as ethanol concentration (%Et), extraction temperature (T), time (t) and solvent volume (V), on extraction yield (Y), total phenolic content (TPC), antioxidant activity (DPPH and FRAP methods) and aloin content, was studied. Optimum extraction conditions were determined as 80% ethanol, 80 °C, 36.6 min and 50 mL and optimized extracts showed interesting contents of polyphenols and antioxidant performance. The phenolic profile was determined by HPLC-DAD/MS and some major phenolic compounds, such as aloin A, aloin B, aloesin, aloe-emodin, aloeresin D, orientin, cinnamic acid and chlorogenic acid, were quantified while eight other compounds were tentatively identified. Moreover, structural and thermal properties were studied by FTIR and TGA analyses, respectively. The obtained results suggested the potential of AVS as a promising source of bioactive compounds, thus increasing the added value of this agricultural waste.