Orthopedic interfaces such as the tendon-bone junction (TBJ) present unique challenges for biomaterials development. Here we describe a multi-compartment collagen–GAG scaffold fabricated via lyophilization that contains discrete mineralized (CGCaP) and non-mineralized (CG) regions joined by a continuous interface. Modifying CGCaP preparation approaches, we demonstrated scaffold variants of increasing mineral content (40 vs. 80 wt% CaP). We report the impact of fabrication parameters on microstructure, composition, elastic modulus, and permeability of the entire multi-compartment scaffold as well as discrete mineralized and non-mineralized compartments. Notably, individual mineralized and non-mineralized compartments differentially impacted the global properties of the multi-compartment composite. Of particular interest for the development of mechanically-loaded multi-compartment composites, the elastic modulus and permeability of the entire construct were governed primarily by the non-mineralized and mineralized compartments, respectively. Based on these results we hypothesize spatial variations in scaffold structural, compositional, and mechanical properties may be an important design parameter in orthopedic interface repair.