A multiscale mathematical model describing the metals biosorption on algal–bacterial photogranules within a sequencing batch reactor (SBR) is presented. The model is based on systems of partial differential equations (PDEs) derived from mass conservation principles on a spherical free boundary domain with radial symmetry. Hyperbolic PDEs account for the dynamics of sessile species and their free sorption sites, where metals are adsorbed. Parabolic PDEs govern the diffusion, conversion and adsorption of nutrients and metals. The dual effect of metals on photogranule ecology is also modelled: metal stimulates the production of EPS by sessile species and negatively affects the metabolic activities of microbial species. Accordingly, a stimulation term for EPS production and an inhibition term for metal are included in all microbial kinetics. The formation and evolution of the granule domain are governed by an ordinary differential equation with a vanishing initial value, accounting for microbial growth, attachment and detachment phenomena. The model is completed with systems of impulsive differential equations describing the evolution of dissolved substrates, metals, and planktonic and detached biomasses within the granular-based SBR. The model is integrated numerically to examine the role of the microbial species and EPS in the adsorption process, and the effect of metal concentration and adsorption properties of biofilm components on the metal removal. Numerical results show an accurate description of the photogranules evolution and ecology and confirm the applicability of algal–bacterial photogranule technology for metal-rich wastewater treatment.