Simultaneous recovery of calcium phosphate granules (CaP granules) and methane in anaerobic treatment of source separated black water (BW) has been previously demonstrated. The exact mechanism behind the accumulation of calcium phosphate (Ca x(PO4) y) in CaP granules during black water treatment was investigated in this study by examination of the interface between the outer anaerobic biofilm and the core of CaP granules. A key factor in this process is the pH profile in CaP granules, which increases from the edge (7.4) to the center (7.9). The pH increase enhances supersaturation for Ca x(PO4) y phases, creating internal conditions preferable for Ca x(PO4) y precipitation. The pH profile can be explained by measured bioconversion of acetate and H2, HCO3- and H+ into CH4 in the outer biofilm and eventual stripping of CO2 and CH4 (biogas) from the granule. Phosphorus content and Ca x(PO4) y crystal mass quantity in the granules positively correlated with the granule size, in the reactor without Ca2+ addition, indicating that the phosphorus rich core matures with the granule growth. Adding Ca2+ increased the overall phosphorus content in granules >0.4 mm diameter, but not in fine particles (<0.4 mm). Additionally, H+ released from aqueous phosphate species during Ca x(PO4) y crystallization were buffered by internal hydrogenotrophic methanogenesis and stripping of biogas from the granule. These insights into the formation and growth of CaP granules are important for process optimization, enabling simultaneous Ca x(PO4) y and CH4 recovery in a single reactor. Moreover, the biological induction of Ca x(PO4) y crystallization resulting from biological increase of pH is relevant for stimulation and control of (bio)crystallization and (bio)mineralization in real environmental conditions.