A water-soluble, blocked diisocyanate was proven to support stable growth of bilayers with branched poly(ethylenimine), bPEI, in a layer-by-layer (LBL) technique. A quartz crystal microbalance and ellipsometry were employed to measure bilayer formation and infrared spectroscopy of LBL deposited films of hexamethylene-1,6-di(aminocarboxysulfonate) and bPEI revealed in situ cross-linking between successive layers. Erratic film growth with poly(diallyldimethylammonium chloride) with which covalent linkage was not possible, and film stability in high salt and diethanolamine solutions also supported cross-linking. Silica beads coated with alkaline phosphatase (ALP)-bPEI bilayers were capped with the cross-linking agent, and loss of enzymatic activity and less dissolution of active ALP were observed, relative to uncapped or alternately caped assemblies. Consequently, such a cross-linking agent alone or diluted with other polyanions, like poly(sodium 4-styrenesulfonate), might prove useful in controlling network and dissolution properties of LBL films having a variety of biologic and other functions, such as for controlled release.