Objective: Microbial transformations are green biotechnological processes where different microorganisms or enzymes are used to produce new metabolites from defined substrates. Hesperidin, quercetin, and their derivatives have been proven in scientific research to have a variety of biological activities, such as antioxidant, antimicrobial, and anticancer activities. Material and Method: This study performed the microbial transformation of hesperidin and quercetin utilizing 13 different microbial strains. The transformation extracts of hesperidin and quercetin were investigated in antioxidant (DPPH· and ABTS·+ methods) and anti-inflammatory effects. Result and Discussion: The biotransformation of hesperidin was observed in 5 of 13 strains. There were Rhizopus stolonifera, Saccharomyces pararoseus, S. cerevisiae, Penicillium claviforme, and Fusarium solani while microbial transformation of quercetin was identified Aspergillus flavus and Penicillium claviforme. The results of this research show that the extracts obtained with the Aspergillus and Penicillium strains were more effective in terms of antioxidant and anti-inflammatory effects. DPPH· antioxidant activity of A. flavus extract (IC50: 22.55±0.32 µg/ml) was higher than the other biotransformation extracts. The IC50 value of R. stolonifer from the hesperidin transformation extracts is 25.93±0.36 µg/ml. The microbial transformation of hesperidin by Penicillium strain has not been researched previously.