Solar-driven water splitting is a key photochemical reaction that underpins the feasible and sustainable production of solar fuels. An amorphous cobalt-phosphate catalyst (Co-Pi) based on earth-abundant elements has been recently reported to efficiently promote water oxidation to protons and dioxygen, a main bottleneck for the overall process. The structure of this material remains largely unknown. We here exploit ab initio and classical atomistic simulations combined with metadynamics to build a realistic and statistically meaningful model of Co-Pi nanoparticles. We demonstrate the emergence and stability of molecular-size ordered crystallites in nanoparticles initially formed by a disordered Co-O network and phosphate groups. The stable crystallites consist of bis-oxo-bridged Co centers that assemble into layered structures (edge-sharing CoO(6) octahedra) as well as in corner- and face-sharing cubane units. These layered and cubane motifs coexist in the crystallites, which always incorporate disordered phosphate groups at the edges. Our computational nanoparticles, although limited in size to ~1 nm, can contain more than one crystallite and incorporate up to 18 Co centers in the cubane/layered structures. The crystallites are structurally stable up to high temperatures. We simulate the extended X-ray absorption fine structure (EXAFS) of our nanoparticles. Those containing several complete and incomplete cubane motifs-which are believed to be essential for the catalytic activity-display a very good agreement with the experimental EXAFS spectra of Co-Pi grains. We propose that the crystallites in our nanoparticles are reliable structural models of the Co-Pi catalyst surface. They will be useful to reveal the origin of the catalytic efficiency of these novel water-oxidation catalysts.