We study the projected gradient descent method on low-rank matrix problems with a strongly convex objective. We use the Burer-Monteiro factorization approach to implicitly enforce low-rankness; such factorization introduces non-convexity in the objective. We focus on constraint sets that include both positive semi-definite (PSD) constraints and specific matrix norm-constraints. Such criteria appear in quantum state tomography and phase retrieval applications. We show that non-convex projected gradient descent favors local linear convergence in the factored space. We build our theory on a novel descent lemma, that non-trivially extends recent results on the unconstrained problem. The resulting algorithm is Projected Factored Gradient Descent, abbreviated as ProjFGD, and shows superior performance compared to state of the art on quantum state tomography and sparse phase retrieval applications.