Phthalocyanines (Pc) are dyes in widespread use in materials science and nanotechnology, with numerous applications in medicine, photonics, electronics and energy conversion. With the aim to construct biohybrid materials, we here prepared and analyzed the structure of two Pc-loaded virus-like particles (VLP) with diameters of 20 and 28 nm (i.e., T = 1 and T = 3 icosahedral symmetries, respectively). Our cryo-electron microscopy (cryo-EM) studies show an unprecedented, very high level of Pc molecule organization within both VLP. We found that 10 nm diameter nanospheres form inside the T = 1 VLP by self-assembly of supramolecular Pc stacks. Monodisperse, self-assembled organic dye nanospheres were not previously known, and are a consequence of capsid-imposed symmetry and size constraints. The Pc cargo also produces major changes in the protein cage structure and in the mechanical properties of the VLP. Pc-loaded VLP are potential photosensitizer/carrier systems in photodynamic therapy (PDT), for which their mechanical behaviour must be characterized. Many optoelectronic applications of Pc dyes, on the other hand, are dependent on dye organization at the nanoscale level. Our multidisciplinary study thus opens the way towards nanomedical and nanotechnological uses of these functional molecules.