In this study, an efficient utilization and valorization of mandarin peel (Citrus unshiu Marc. var. Kuno) was investigated using innovative and green extraction techniques. The first step of this study included the extraction and analysis of the volatile compounds by performing a supercritical CO2 (SC-CO2) extraction under different operating pressure conditions (100 and 300 bar). The analysis of volatile compounds of the obtained extracts was conducted by gas chromatography-mass spectrometry (GC-MS), and limonene was found to be the dominant volatile component (13.16% at 100 bar; 30.65% at 300 bar). After SC-CO2 treatment, the exhausted citrus peel waste enriched with bioactive compounds was subjected to subcritical water extraction (SWE) in a wide temperature range (130–220 °C) using different solvent-solid ratio (10–30 mL/g) in time periods from 5 to 15 min, in order to obtain bioflavonoids. Identification and quantification of present bioflavonoids was conducted by high-performance liquid chromatography with a with a diode array detector (HPLC), and hesperidin (0.16–15.07 mg/g) was determined as the most abundant flavanon in mandarin peel with other polyphenolic compounds that were possible by-products of thermal degradation. At higher temperatures, the presence of 5-hydroxymethylfurfural (5-HMF) and chlorogenic acid were detected. Antiradical activity and total phenolic content in the extracts were determined using spectrophotometric methods, while the process optimization was performed by response surface methodology (RSM).