In this study, the synthesis of a series of bay-substituted donor–acceptor–donor (D–A–D) type perylene diimide derivatives (3a–3d) has been reported as an acceptor for the small-molecule-based organic solar cells (SM-OSCs) by the Suzuki coupling method. It has been evaluated for the antimicrobial activity against some of the bacteria and fungi. The synthesised SMs were confirmed by Fourier transform-infrared spectroscopy, nuclear magnetic resonance (NMR), and high resolution mass spectroscopy (HR-MS). The SMs showed absorption up to 750 nm, which eventually reduced the optical band gap Egopt to < 2 eV. SMs showed thermal stability up to 400 °C. In the SM-OSC, the SMs showed a power conversion efficiency of < 1% with the P3HT donor in bulk hetero-junction device structure. Additionally, the new SMs showed antimicrobial activity against Gram-negative bacteria such as Escherichia coli Gram-positive bacteria such as Bacillus subtilis and antifungal activity against the Candida albicans, and Aspergillus Niger. Cytotoxicity studies were carried out against the breast cancer cell lines MCF-7 using MTT assay method. The results revealed that the SMs was able to inhibit the cancer cells. LD50s calculated for the SMs 3a–3d were between 200 and 400 µg/ml.