In the current study, we synthesized and characterized new BODIPY derivatives (1–4) having pyridine or thienyl‐pyridine substituents at meso‐ position and 4‐dibenzothienyl or benzo[b]thien‐2‐yl moieties at 2‐,6‐ positions. We investigated fluorescence properties and the ability to form singlet oxygen. In addition, various biological activities of BODIPYs such as DPPH scavenging, DNA binding/cleavage ability, cell viability inhibition, antimicrobial activity, antimicrobial photodynamic therapy (aPDT) and biofilm inhibition properties were performed. BODIPY derivatives BDPY‐3 (3) and BDPY‐4 (4) have high fluorescence quantum yields as 0.50 and 0.61 and 1O2 quantum yields were calculated as 0.83 for BDPY‐1 (1), 0.12 for BDPY‐2 (2), 0.11 for BDPY‐3 and 0.23 for BDPY‐4. BODIPY derivatives BDPY‐2, BDPY‐3 and BDPY‐4 displayed 92.54 ± 5.41%, 94.20 ± 5.50%, and 95.03 ± 5.54% antioxidant ability, respectively. BODIPY compounds showed excellent DNA chemical nuclease activity. BDPY‐2, BDPY‐3 and BDPY‐4 also exhibited 100% APDT activity against E. coli at all tested concentrations. In addition to these, they demonstrated a highly effective biofilm inhibition activity against Staphyloccous aureus and Pseudomans aeruginosa. BDPY‐4 showed the most effective antioxidant and DNA cleavage activity, while BDPY‐3 exhibited the most effective antimicrobial and antibiofilm activity.