The worldwide threat of antibiotic resistance requires alternative strategies to fight bacterial infections. A promising approach to support conventional antibiotic therapy is the antimicrobial photodynamic inactivation (aPDI). The aim of this work was to show further insights into the antimicrobial photodynamic principle using two photosensitizers (PS) of different chemical classes, Methylene Blue (MB) and TMPyP, and the organisms Escherichia coli and Staphylococcus aureus as Gram-negative and Gram-positive representatives. Planktonic cultures of both species were cultured under aerobic conditions for 24 h followed by treatment with MB or TMPyP at various concentrations for an incubation period of 10 min and subsequent irradiation for 10 min. Ability to replicate was evaluated by CFU assay. Accumulation of PS was measured using a spectrophotometer. The cytoplasmic membrane integrity was investigated by flow cytometry using SYBR Green and propidium iodide. In experiments on the replication ability of bacteria after photodynamic treatment with TMPyP or MB, a killing rate of 5 log(10) steps of the bacteria was achieved. Concentration-dependent accumulation of both PS was shown by spectrophotometric measurements whereby a higher accumulation of TMPyP and less accumulation of MB was found for S. aureus as compared to E. coli. For the first time, a membrane-damaging effect of TMPyP and MB in both bacterial strains could be shown using flow cytometry analyses. Furthermore, we found that reduction of the replication ability occurs with lower concentrations than needed for membrane damage upon MB suggesting that membrane damage is not the only mechanism of aPDI using MB.