Oranges and mandarins in Chongqing, China, are mostly processed for juice and their peels are wasted or landfilled. To add value, it is essential to utilize the peels and extract useful materials, such as citrus essential oils (CEOs). Here, we report the metabolome analysis of the peels of Citrus x sinensis (CS) and Citrus reticulata (CR). In total, 793 metabolites were detected in the CS and CR peels, of which 242 were differentially accumulated. The metabolites were grouped into 12 compound classes. Terpenoids were the highest accumulated class of compounds followed by phenols and alcohols in both fruit peels. CR peels were rich in all types of compounds, whereas CS showed a relatively lower content of the detected compounds. The highest accumulated compounds were β-phellandrene, beta-ocimene, 1,3,6-octatriene,3,7-dimethyl, and d-limonene. Overall, CR showed higher compound diversity than CS. The CS and CR peel extracts showed antibacterial effects against Escherichia coli, Staphylococcus aureus, and Bacillus subtilis. The peel extracts from CR and CS showed similar antibacterial effects against E. coli and B. subtilis, while CS peel extracts were more effective against S. aureus. Overall, our study concludes that both CS and CR peels should not be wasted owing to the CEOs and respective antibacterial activities.