The uptake and phototoxicity of a family of BODIPY-perylene charge transfer dyads are compared in live cancer and non-cancer cell lines to evaluate their performance in imaging and photodynamic therapy (PDT). The impact of iodination and mesylation of the meso position of the compounds on their optical properties, cell uptake and toxicity are compared. Notably, across all derivatives the probes were minimally dark toxic up to 50 μM, (the maximum concentration tested), but exhibited outstanding phototoxicity with nanomolar IC50 values and impressive phototoxic indices (PI, ratio of dark IC50 to light IC50), with best performance for the mesylated iodinated derivative MB2PI, which had a PI of >218 and >8.9 in MCF-7 cells and tumour spheroids respectively. This is significantly higher than non-iodinated analogue MB2P in MCF-7 cells with an observed PI of >109 and slightly higher than MB2PI in spheroids with a PI of >8. This compound also showed interesting emission spectral variation with localisation that responded to stimulation of inflammation. Additional studies confirmed efficient singlet oxygen generation by the BODIPYs, suggesting a Type II mechanism of phototoxicity. Overall, the data indicates that combining charge transfer and iodination is an effective strategy for enhancing phototherapeutic capacity of BODIPY PS.