Chemical cross-linking of layer-by-layer assembled films promotes mechanical stability and robustness in a wide variety of environments, which can be a challenge for polyelectrolyte multilayers in saline environments or for multilayers made from weak polyelectrolytes in environments with extreme pHs. Heating branched poly(ethylenimine)/poly(acrylic acid) (BPEI/PAA) multilayers at sufficiently high temperatures drives amidization and dehydration to covalently cross-link the film, but this reaction is rather slow, typically requiring heating for hours for appreciable cross-linking to occur. Here, more than one order of magnitude increase in the amidization kinetics is realized through microwave heating of BPEI/PAA multilayers on indium tin oxide (ITO)/glass substrates. The cross-linking reaction is tracked using infrared spectroscopic ellipsometry to monitor the development of the cross-linking products. For thick films (similar to 1500 nm), gradients in cross-link density can be readily identified by infrared ellipsometry. Such gradients in cross-link density are driven by the temperature gradient developed by the localized heating of ITO by microwaves. This significant acceleration of reactions using microwaves to generate a well-defined cross-link network as well as being a simple method for developing graded materials should open new applications for these polymer films and coatings.