While biological crystallization processes have been studied on the microscale extensively, models addressing the mesoscale aspects of such phenomena are rare. In this work, we investigate whether the phase-field theory developed in materials science for describing complex polycrystalline structures on the mesoscale can be meaningfully adapted to model crystallization in biological systems. We demonstrate the abilities of the phase-field technique by modeling a range of microstructures observed in mollusk shells and coral skeletons, including granular, prismatic, sheet/columnar nacre, and sprinkled spherulitic structures. We also compare two possible micromechanisms of calcification: the classical route via ion-by-ion addition from a fluid state and a non-classical route, crystallization of an amorphous precursor deposited at the solidification front. We show that with appropriate choice of the model parameters microstructures similar to those found in biomineralized systems can be obtained along both routes, though the timescale of the non-classical route appears to be more realistic. The resemblance of the simulated and natural biominerals suggests that, underneath the immense biological complexity observed in living organisms, the underlying design principles for biological structures may be understood with simple math, and simulated by phase-field theory.