Food waste represents a major global environmental and economic challenge, particularly within the food processing industry, including fruit and juice manufacturing and canteens, where significant amounts of peel and pomace residues are generated annually without effective valorization. This study evaluated the potential of mango, orange, and pineapple peel wastes as sustainable sources of functional ingredients. Fruit peel samples collected from university canteens were processed into flours and subjected to Soxhlet extraction (ethanol/water, 70:30, v/v), followed by concentration under reduced pressure. Antioxidant activity was assessed using DPPH and FRAP assays, while free sugars, organic acids, and phenolic compounds were characterized by HPLC-RI-PDA. Antimicrobial activity against Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, and Pseudomonas aeruginosa was evaluated using agar diffusion and broth microdilution methods. Statistical analysis was performed by one-way ANOVA followed by Tukey’s HSD test (p < 0.05). The results demonstrated a clear relationship between phytochemical composition and bioactivity. Mango peel extract showed the highest antioxidant capacity, associated with higher levels of phenolic compounds, flavonoids, and organic acids, including caffeic, p-coumaric, ferulic, and ellagic acids, as well as rutin, apigenin, and myricetin and a stronger antimicrobial performance. Orange peel extract was characterized by higher levels of naringin, procyanidin, and synaptic acid, whereas pineapple peel extract showed higher kaempferol content, corresponding to moderate bioactivity. Overall, mango and pineapple peel extracts exhibited the most pronounced antimicrobial effects against all tested bacterial strains. Furthermore, the remaining biomass after extraction demonstrated potential for composting and conversion into organic fertilizer, supporting integrated waste valorization strategies. The findings indicate that fruit peel wastes from industrial processing represent promising and sustainable sources of bioactive compounds that could be explored for the development of functional ingredients for food, nutraceutical, and pharmaceutical applications, while contributing to circular economy approaches and supporting Sustainable Development Goals 2, 9, and 12.