A series of new 1,4-naphtho- and benzoquinone derivatives possessing N-, S-, O-substituted groups which has not been reported yet has been synthesized from 2,3-dichloro-1,4-naphthoquinone 1 and 2,3,5,6-tetrachlorocyclohexa-2,5-diene-1,4-dione 15 involving a Michael addition. In the synthesized compounds, antimicrobial activity at low concentrations against Escherichia coli B-906, Staphylococcus aureus 209-P, and Mycobacterium luteum B-917 bacteria and Candida tenuis VKM Y-70 and Aspergillus niger F-1119 fungi in comparison with controls was identified. 2-Chloro-3-((2-(piperidin-1-yl)ethyl)amino)naphthalene-1,4-dione 3g and 2,5-dichloro-3-ethoxy-6-((2,4,6-trifluorophenyl)amino)cyclohexa-2,5-diene-1,4-dione 17 were the most potent, with a minimum inhibitory concentration value of 15.6 mu g/mL against test-culture M. luteum and S. aureus, respectively. Furthermore, in this work, a catalase activity of benzo- and naphthoquinone derivatives was examined for the first time. The catalase activity of benzo- and naphthoquinone derivatives was determined, showing that compound 3g had significant inhibition activity for catalase enzyme.