Poly(dimethylsiloxane) (PDMS) microbioreactors with computerized perfusion controls would be useful for engineering the bone marrow microenvironment. However, previous efforts to grow primary bone marrow cells on PDMS substrates have not been successful due to the weak attachment of cells to the PDMS surface even with adsorption of cell adhesive proteins such as collagen or fibronectin. In this work, modification of the surface of PDMS with biofunctional multilayer coatings is shown to promote marrow cell attachment and spreading. An automated microfluidic perfusion system is used to create multiple types of polyelectrolyte nanoscale coatings simultaneously in multiple channels based on layer-by-layer deposition of PDDA (poly(diallyldimethyl ammonium chloride)), clay, type IV collagen and fibronectin. Adherent primary bone marrow cells attached and spread best on a surface with composition of (PDDA/clay)5 (Collagen/Fibronectin)2 with negatively charged fibronectin exposed on the top, remaining well spread and proliferating for at least two weeks. Compared to traditional more macroscopic layer-by-layer methods, this microfluidic nanocomposite process has advantages of greater flow control, automatic processing, multiplexed fabrication, and use of lesser amounts of polymers and protein solutions.