Natural biopolymers such as human fibrin are appealing to tissue engineers, because fibrin is biocompatible, bioresorbable, and essential in normal wound healing. There have been numerous studies to date to develop a fibrin-based injectable cell delivery system, albeit with varying success. We propose that the outcome of fibrin cell delivery can, in part, be attributed to the relative concentrations of fibrinogen and thrombin solutions (i.e., formulations) and the structure of the final 3D fibrin clot. Formulation-dependent proliferation of human mesenchymal stem cells (hMSCs) within 3D fibrin clots was investigated in vitro. Our results indicate that hMSCs are viable in all fibrin sealant formulations investigated, and proliferation rates vary with fibrin formulations. Furthermore, the fibrinogen solution, not thrombin, was found to have a more dominant role on hMSC proliferation, with dilute fibrinogen solutions promoting greater hMSC proliferation. Confocal and electron microscopy reveal formulation dependence on 3D fibrin clot structure, with dilute fibrinogen solutions yielding more open, homogeneous microstructures. This study suggests that the concentrations of fibrinogen and thrombin solutions must be carefully considered for cell delivery because they affect 3D fibrin clot structure and cell proliferation.