Destruction of unwanted cells and tissues in photodynamic therapy (PDT) is achieved by a combination of light, oxygen, and light-sensitive molecules. The advantages of PDT compared to other traditional treatment modalities, and the shortcomings of the currently used photosensitizers, have stimulated the search for new, more efficient photosensitizer candidates. Ability to inflict selective damage to particular proteins through photo-irradiation would significantly advance the design of highly specific photosensitizers. Achieving this objective requires comprehensive knowledge concerning the interactions of the particular photosensitizer with specific targets. Here, we summarize the effects of Zn(II) N-alkylpyridylporphyrin-based photosensitizers on intracellular (metabolic, antioxidant and mitochondrial enzymes) and membrane proteins. We emphasize how the structural modifications of the porphyrin side substituents affect their lipophilicity, which in turn influence their subcellular localization. Thus, Zn(II) N-alkylpyridylporphyrins target particular cellular sites and proteins of interest, and are more efficient than hematoporphyrin D, whose commercial preparation (Photofrin) has been clinically approved for PDT.