Three-dimensional nanocomposites prepared using two different families of nanomaterials holds significant relevance pertaining to biological applications. However, integration of the two distinct nanomaterials with precision to control the overall compositional homogeneity of the resulting 3D nanocomposite is a synthetic challenge. Conventional reactions result in nanocomposites with heterogeneous composition and render useless. To address this challenge, we have developed a fluidics-mediated process for controlling the interaction of nanoparticles to yield a compositional uniform multidimensional nanoparticle; as an example, we demonstrated the integration of gold nanoparticles on gelatin nanoparticles. The composition of the nanocomposite is controlled by reacting predetermined number of gold nanoparticles to a known number of thiolated gelatin nanoparticles at any given time within a defined cross-sectional area. Using the fluidics process, we developed nanocomposites of different composition: [gelatin nanoparticles-(gold, nanoparticles)(x)] where x(average) = 2, 12, or 25. The nanocomposites were further surface conjugated with organic molecules such as fluorescent dye Or polyethylene glycol (PEG) molecules. To study the biological behavior of nanocomposite, we investigated the cellular internalization and trafficking characteristics of nanocomposites in two human cancer cell lines. The nanocomposites exhibited a three-stage cellular release mechanism that enables the translocation of gold nanoparticles within various cellular compartments. In summary; the three-dimensional nanocomposite serves as a novel platform for developing well-defined protein-metal nanocomposites for potential drug delivery, sensory, and molecular imaging applications.