Owing to their great quantity of various phytochemicals we aimed to investigate the phytochemical composition of ginger and lemon peel aqueous and ethanolic extracts, their potential antimicrobial activity, and anticancer properties. Ginger peel powder possesses the highest phytochemical content compared to lemon peels. The maximum phenolic and flavonoid contents of ginger were extracted in ethanolic extracts, which were documented as 20.65 mg GAE/g and 12.96 mg QC/g compared to lemon peel extracts. Additionally, ethanolic and aqueous ginger peel extracts exhibited superior antioxidant activity (96.91 and 95.77%, respectively) compared to lemon peel extract. HPLC fractionation further revealed the diverse phenolic and flavonoid compounds present in both peels, with ethanolic extracts consistently outperforming their aqueous ones. The ethanolic extracts of both ginger and lemon peels exhibit a higher degree of antimicrobial activity compared to their aqueous extract. Notably, the ethanolic extract of ginger peels demonstrates remarkable inhibition zones, particularly against gram-positive bacteria and gram-negative bacteria. On the other hand, ethanolic extracts of both peels exhibited potent cytotoxic effects against liver and colon carcinoma cells, with ethanolic extract of ginger peel showing superior anticancer potential with IC50 (4.7 and 5.2 µg/ml, respectively). Apoptotic and necrotic cell analyses underscored the ability of ginger peel ethanolic extract to induce a higher level of cancer cell apoptosis while minimizing necrosis. Therefore, our study lies in the distinct phytochemical profile of ginger and lemon peel extracts, emphasizing the higher phenolic and flavonoid contents in ethanolic extracts and their effect as antimicrobial and anticancer activity.