Decomposition of endoperoxide containing molecules is an attractive approach for the delayed release of singlet oxygen under mild reaction conditions. Here we describe a new method for the adaptation of the corresponding decay times by controlling the supramolecular functional structure of the surrounding matrix in the immediate vicinity of embedded singlet oxygen precursors. Thus, a significant prolongation of the lifetime of the endoperoxide species is possible by raising the energy barrier of the thermal O-1(2)-releasing step via a restriction of the free volume of the applied carrier material. Enabling such a prolonged decomposition period is crucial for potential biomedical applications of endoperoxide containing molecules, since sufficient time for appropriate cell uptake and transport to the desired target region must be available under physiological conditions before the tissue damaging-power of the reactive oxygen species formed is completely exhausted. Two novel polyaromatic systems for the intermediate storage and transport of endoperoxides and the controlled release of singlet oxygen in the context of anticancer and antibiotic activity have been prepared and characterized. These compounds are based on functionalized derivatives of the 1,4-dimethylnaphthalene family which are readily forming metastable endoperoxide species in the presence of dioxygen, a photosensitizer molecule such as methylene blue and visible light. In contrast to previously known systems of similar photoreactivity, the endoperoxide carrying molecules have been designed with optimized molecular properties in terms of potential chemotherapeutic applications. These include modifications of polarity to improve their incorporation into various biocompatible carrier materials, the introduction of hydrogen bonding motifs to additionally influence the endoperoxide decay kinetics, and the synthesis of bifunctional derivatives to enable synergistic effects of multiple singlet oxygen binding sites with an enhanced local concentration of reactive species. With these compounds, a promising degree of endoperoxide stability adjustment within the carrier matrix has been achieved (polymer films or nanoparticles), which now opens the stage for appropriate targeting of the corresponding pro-drugs into live cells. First results on cytocidal and cytostatic properties of these compounds embedded in ethylcellulose nanoparticles are presented. Furthermore, an efficient low-cost method for the photochemical production of reactive endoperoxides based on high-power 660 nm LED excitation at room temperature and ambient conditions in ethanol solution is reported.