1,4‐Naphthoquinones are an important class of compounds present in a number of natural products. In this study, a new series of 1,4‐naphthoquinone derivatives were synthesized. All the synthesized compounds were tested for in vitro antimicrobial activity. In this present investigation, two Gram‐positive and five Gram‐negative bacterial strains and one pathogenic yeast strain were used to determine the antibacterial activity. Naphthoquinones tested for its antibacterial potencies, among seven of them displayed better antimicrobial activity against Staphylococcus aureus (S. aureus; 30–70 μg/mL). Some of the tested compounds showed moderate to low antimicrobial activity against Pseudomonas aeruginosa (P.aeruginosa) and Salmonella bongori (S. bongori; 70–150 μg/mL).