Spray-assisted layer-by-layer (LbL) assembly is far more rapid than conventional dip-assisted assembly methods and has gained widespread interest recently. Even so, it has remained unclear as to how the structure and properties of the resulting LbL film vary with processing method. Here, we compared the thermal properties of poly(ethylene oxide) (PEO)/poly(acrylic acid) (PAA) and PEO/poly(methacrylic acid) (PMAA) hydrogen-bonded LbL assemblies prepared using both dip-assisted and spray-assisted deposition methods. While the surface morphologies of PEO/PAA LbL assemblies were similar, those of PEO/PMAA LbL assemblies were greatly influenced by deposition method. In both PEO/PAA and PEO/PMAA LbL assemblies, glass transition temperatures were not influenced by deposition method, but the transition's breadth was consistently larger for the spray-assisted LbL films. These results indicate that the internal structure of spray-assisted LbL films is slightly more heterogeneous, possibly arising from the shorter time scale of deposition.