The peels from three pumpkin genotypes cultivated in Greece were assessed for their phenolic content and bioactive properties to obtain extracts with a high preservative capacity. The optimization of the extraction was performed through response surface methodology (RSM) based on a Box–Behnken experimental design after applying two extraction techniques: heat-assisted (HAE) and ultrasound-assisted (UAE) extraction. The implemented independent variables were time, solvent concentration, and temperature/power (for HAE/UAE), while as dependent variables the dry residue (DR), reducing power (RP), and total phenolic content (TP) were considered. In general, HAE was the most effective technique for ‘TL’ (75 min; 30 °C; 24% ethanol) and ‘Voutirato’ (15 min; 30 °C; 10% ethanol), while UAE was more effective for ‘Leuka Melitis’ (5 min; 400 W; 0% ethanol). The extracts obtained in the global optimum conditions for each genotype peel were then assessed for their phenolic profile, by HPLC-DAD-ESI/MS, and bioactive potential. Seven phenolic compounds were detected, including four flavonoids, two phenolic acids, and one flavan-3-ol. The extracts presented high antioxidant, antibacterial, and antifungal potential, with no cytotoxicity for non-tumor cells. The optimized conditions for the extraction of preservative compounds from bioresidues were defined, allowing the acquisition of antioxidant and antimicrobial extracts and proving their potential for food application.