A biomimetic reactor has been developed to synthesize hydroxyapatite-gelatin (HAP-GEL) nanocomposites that mimic ultra-structures of natural bone. We hypothesize that in the reactor, gelatin concentration controls morphology and packing structures of HAP crystals. To test the hypothesis, three types of mechanical tests were conducted, including nanoindentation, compression, and fracture tests. Nanoindentation tests in conjunction with computer modeling were used to assess effects on gelatin-induced microstructures of HAP. The results showed that increasing gelatin content increased both the plane strain modulus and the fracture toughness. The gelatin appeared to shorten the HAP crystal distance, which consolidated the internal structure of the composite and made the material more rigid. The fracture toughness KIC increased partially due to the effect of fiber bridging between gelatin molecules. The highest fracture toughness (1.12 MPa·m1/2) was equivalent to that of pure hydroxyapatite. The compressive strength of the HAP-GEL (107.7±6.8 MPa) was, however, less sensitive to microstructural changes and was within the range of natural cortical bone (human 170 MPa, pig: 100 MPa). The compression strength was dominated by void inclusions while the nanoindentation response reflected ultra-structural arrangement of the crystals. The gelatin concentration is likely to modify crystal arrangement as demonstrated in TEM experiments but not void distribution at macroscopic levels.