This study reports the synthesis of three silicon phthalocyanines (SiPc1–3) bearing 2‐dimethylaminoethoxy, 2‐[2‐(dimethylamino)ethoxy]ethoxy, or 2‐{2‐[2‐(dimethylamino)ethoxy]ethoxy}ethoxy on axial positions. Also, their quaternized derivatives (SiPcQ1–3) were prepared. The effect of ligand length on the biological features of water‐soluble silicon phthalocyanines (SiPcQ1–3) was investigated. The highest antimicrobial activity was obtained 32 μg/mL for SiPcQ1 against double‐distilled water, E. hirae, and E. faecalis. The growth inhibition percentages of compounds SiPcQ1–3 were obtained 100 %, 100 %, and 85.14 %, respectively. The highest biofilm inhibition activity was obtained 86.16 % for 250 mg/L SiPcQ3 against S. aureus. The E. coli growth inhibition activities of 50 mg/L compounds SiPcQ1–3 ranged from 60.17 % to 87.53 % and their activities increased (73.46 %–95.37 %) by the enhancement of the concentration. The E. coli viability inhibition activities of SiPcQ1–3 were concentration‐dependent. The DNA cleavage and binding properties of SiPcQ1–3 were studied using pBR322 DNA and CT‐DNA, respectively. Besides, the toxicity of SiPcQ1–3 was examined against the human colon cancer cell line (DLD‐1). The IC50 values of compounds (SiPcQ1–3) were obtained between 10.12 and 27.06 μM in the dark, however, these values were calculated between 12.32 and 22.17 μM under the light. SiPcQ3 exhibited the highest in vitro anticancer activity against the tested cell.