Background: The search of the approaches towards a photosensitizer’s conjugation with multifunctional nanoparticles is an important step in the development of photodynamic therapy techniques. Association of photosensitizer molecules with nanoparticles that perform the delivery function can lead to a change in the functional state of the photosensitizer. Methods: We studied the effects observed upon incorporation of octa- and hexadeca-carboxyphthalocyanines of zinc(II) and aluminum(III) (Pcs) into the polymer shell of nanoparticles with a semiconductor CdSe/CdS/ZnS core with various spectral and optical methods. Results: First, the interaction of Pc with the polymer shell leads to a change in the spectral properties of Pc; the effect strongly depends on the structure of the Pc molecule (number of carboxyl groups as well as the nature of the central cation in the macrocycle). Secondly, upon incorporation of several Pc molecules, concentration effects become significant, leading to Pc aggregation and/or nonradiative energy transfer between neighboring Pc molecules within a single nanoparticle. Conclusions: These processes lead to the decrease of a number of the Pc molecules in an excited state. Such effects should be taken into account during the development of multifunctional platforms for the delivery of photosensitizers, including the use of nanoparticles as enhancers of photosensitizer activity by energy transfer.