Amino acid derivatives of monascus pigments were produced by fermentation, and their antimicrobial activities were determined. Thirty-nine l- and d-forms of amino acids were added as a precursor to the fermentation medium for derivation of pigments. Derivatives with l-Phe, d-Phe, l-Tyr, and d-Tyr exhibited high activities against Gram+ and Gram− bacteria with MIC values of c. 4–8 μg mL−1. The control red pigment exhibited minimal inhibitory concentration (MIC) values higher than 32 μg mL−1. Derivatives with l-Asp, d-Asp, l-Tyr, and d-Tyr were effective against the filamentous fungi Aspergillus niger, Penicillium citrinum, and Candida albicans. Monascus derivatives of amino acids having a phenyl ring like Phe and Tyr derivatives showed high antimicrobial activities. Incubation of the l-Phe derivative with Bacillus subtilis caused cells to aggregate with formation of pellets. Easy adsorption of the l-Phe pigment derivative to the surface of Escherichia coli cells was observed via SEM and TEM. Addition of monascus pigment derivatives decreased the oxygen uptake rate of E. coli in culture. The antimicrobial activities of pigment derivatives are considered to be related to the reduced availability of oxygen for the cells adsorbed with pigment.