Phosphonates are important organophosphorus compounds which exhibit versatile properties in organic chemistry, medicinal chemistry, materials and biological applications. Phosphonate groups have appeared in a very few examples of BODIPY (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) compounds that are important florescent dyes in these areas. The deficiency in the area motivated us to investigate how the phosphonate substituent(s) affect the structural, electronic, and optical properties of meso, alpha, or alpha, alpha '-substituted BODIPYs using density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods. We have identified the suitable method as HSEH1PBE functional in combination with the basis set 6-31+G** by comparing the theoretical results with the experimental studies. Structural, electronic and optical parameters of a series of designed phosphonate substituted 12 BODIPYs (1-4) have been investigated. The alpha, and alpha, alpha '-vinyl phosphonate substituted BODIPYs (3,4) compared to meso-substituted BODIPYs (1,2) have both lower HOMO/LUMO electronic energies [(-5.57)-(-6.19)/(-3.16)-(-3.91)] and lower electronic energy gaps (E-gap) (2.11-2.42). Electrostatic potential analysis was performed for all BODIPYs to characterize their electron distribution and TD-DFT analysis was used for the absorption spectral analysis. The presented theoretical approach can be a practical guide for experimental studies for the design of new BODIPY compounds with desired properties.