The behavior of pectin and thermally denatured whey proteins at both different protein/polysaccharide ratios and different pH values was investigated. Our findings suggest the formation at pH 5.1 (complexation pH) of transglutaminase-catalyzed cross-links among soluble ionic whey protein/pectin complexes, which could be responsible for the observed increase of both tensile strength (2-fold) and elongation to break (10-fold) of films obtained in the presence of enzyme. Conversely, a significant reduction of elasticity, probably due to the formation of covalent bonds among single whey protein molecules, was observed when the films were prepared in the presence of the enzyme at pH 6.0. In addition, the presence of the enzyme at complexation pH significantly reduced film permeability. Atomic force and scanning electron microscopy revealed significant changes in the microstructure of the films prepared in the presence of TGase as well as in the morphology of their surface.