Benzothiophene derivatives were synthesized regioselectively using coupling reactions and electrophilic cyclization reactions. Antimicrobial properties of isolated compounds were tested against indicator microorganisms such as C. albicans ATCC 10231, B. subtilis ATCC 6633, E. coli ATCC 25922 and S. aureus ATCC 25923. 3-(4-aminobenzoethynyl)-2-(thiophen-2-yl) benzo[b]thiophene (12E), 3-ethynyl-2-(thiophen-2-yl) benzo[b]thiophene (12L) and 3-(2-aminobenzoethynyl)-2-(thiophen-2-yl) benzo[b]thiophene (12J) displayed high antibacterial activity against S. aureus. Further, 3-iodo-2-(thiophen-2-yl) benzo[b]thiophene (10) and 3-(trimethylsilylethynyl)-2-(thiophen-2-yl) benzo[b] thiophene (12K) were found to have potentials to be used as antifungal agents against current fungal diseases. Novel 3-(1H-indole-2-yl)-2-(thiophen-2-yl) benzo[b] thiophene (16) and 3-(4-aminobenzoethynyl)-2-(thiophen-2-yl) benzo[b] thiophene (12E) also showed quite high antioxidant capacities with TEAC values of 2.5 and 1.1, respectively; which surpassed the antioxidant capacity of an universally accepted reference of trolox.