Phase separation within polymer networks plays a central role in shaping the structure and mechanics of both synthetic materials and living cells, including the formation of biomolecular condensates within cytoskeletal networks. Previous experiments and theoretical studies indicate that network elasticity can regulate demixing and stabilize finite-sized domains, yet the microscopic origin of this size selection remains elusive. Here, we use coarse-grained molecular dynamics simulations with an implicit solvent to investigate how network architecture controls phase separation and limits domain growth. By systematically varying the network topology as well as the contour length and bending stiffness of its constituent strands, we uncover that finite domains emerge when intrinsic strand- or network-level length scales, such as persistence length or entanglement length, impose local constraints on coarsening. Further, the size of these finite domains is highly correlated with these microscopic network properties, but depends surprisingly little on the network’s bulk elasticity. Taken together, our findings establish a molecular basis for understanding droplet formation in polymer networks, and provide guiding principles for engineering materials and interpreting condensate behavior in cells.