Multimodal composites have the potential to play a crucial role in the development of theranostic agents. Systems with optical and magnetic response can be applied in medicine for both imaging and therapy; however, combining magnetic and luminescent nanoparticles in one entity is challenging. Both the morphology and architecture of the composite, as well as the influence of the magnetic components and matrix on the light-emissive component, must be paid attention. In this study, we demonstrate a design of a composite with advantageous magnetic response and luminescence in green and red regions (excited at 405 and 580 nm, respectively), where biocompatible CaCO3 microspheres were loaded and decorated with luminescent carbon dots (CDs) and magnetite nanoparticles (MNPs). We showed the absence of CDs’ toxicity by the IC50 tests and demonstrated its localization in L1 and L4 stages of C. elegans embryogenesis. We determine the optimal parameters for composite formation to achieve their improved performance and structural stability. The composites were fabricated in several steps, including loading nanoparticles and layer-by-layer application of polyelectrolytes on top of CaCO3. We demonstrated the applicability of the prepared composite microspheres for flow cytometry and showed their potential as multiplexed visualization agents, emphasizing their potential use as promising theranostic agents.