Photodynamic therapy (PDT), especially with the recent advances in photosensitizer design has already been established as a noninvasive technique for cancer treatment. In PDT, photosensitizers (PSs) are targeted to tumor sites either actively or passively, and are irradiated with a laser of appropriate wavelength. The stimulated PSs transfer excitation energy to endogenous oxygen converting it to reactive oxygen species (ROS) that can kill tumor cells. Up to now, numerous nanomaterials tailored to suitable size, have been studied for effective delivery of PSs. Recently, Near IR-based absorbing nanomaterials which have a rising potency to implement light-triggered tumor ablation have attracted much attention since near-IR light in the 650–850 nm range penetrates more deeply in tissues. In addition, imaging of these nanomaterials carrying PSs is very important in order to prevent damage to the healthy tissues upon irradiation. Magnetic resonance imaging (MRI) is a powerful technique due to its excellent spatial resolution and depth for in vivo imaging. In this study, a multidisciplinary approach was utilized to create MRI active, near IR-based functional nanomaterials. This approach involves (i) nanochemistry to prepare silica coated super paramagnetic iron oxide (core-shell) nanoparticles, (ii) organic chemistry to synthesize four different type of near- IR absorbing Bodipy derivatives as PSs, and (iii) spectroscopy to verify singlet oxygen production. Four different type of Bodipy based PSs were covalently attached to MRI active, biocompatible, and nontoxic nanocarriers and generation of singlet oxygen capabilities were evaluated. It was demonstrated that these core-shell nanoparticles are promising delivery vehicles of PSs for the use in diagnosis and therapy.