Lemon processing generates thousands of tons of residues that can be preserved as flours by thermal treatment to obtain phenolic compounds with beneficial bioactivities. In this study, the effect of different drying temperatures (40, 50, 60, 70, 80, 90, 100 and 110 °C) on the Total Phenolic Content (TPC), antioxidant and antimicrobial activities of phenolic compounds present in Citrus. lemon (L.) Burn f waste was determined. Identification and quantification of phenolic compounds were also performed by UPLC-PDA and UPLC-ESI-MS analysis. Eriocitrin (19.79–27.29 mg g⁻¹ DW) and hesperidin (7.63–9.10 mg g⁻¹ DW) were detected as the major phenolic compounds in the flours by UPLC-PDA and confirmed by UPLC-ESI-MS. Antimicrobial activity determined by Minimum Inhibitory Concentration (MIC) against Salmonella typhimurium, Escherichia coli and Staphylococcus aureus was observed. Accordingly, a stable functional flour as a source of bioactive phenolic compounds obtained from lemon residues at 50 °C may be produced as a value-added product useful in various industrial sectors.