This study sheds light on the potential of microbial transglutaminase (mTG)-mediated modification to enhance the properties of heat-denatured whey protein-based films. In this study, we investigated the biochemical modification of heat-denatured whey proteins (WPs) using mTG, an enzyme known for the ability of crosslinking reactions. By introducing ε-(γ-glutamyl)-lysine crosslinks via an acyl transfer reaction, mTG enhances the properties of bio-based materials. In this research, heated WPs were demonstrated to effectively serve as mTG substrates. The preparation of crosslinked bio-based material was achieved using a casting method under alkaline conditions (pH 12) in the presence of glycerol (40% w/w), which was added as a plasticizer to the film-forming solution (FFS). A comprehensive characterization of the FFSs and the resulting materials was carried out. The FFSs were quite stable as evidenced by Zeta potential values that were always around 30/40 mV regardless of the presence of the enzyme. The enzymatic modification increased the elongation at break of the materials from 10.4 ± 4.9 MPa to 27.6 ± 8.9 MPa, while decreasing both tensile strength and Young’s modulus, thereby making the resulting material more extensible. On the other hand, the enzyme affected both the CO2 and O2 barrier properties, with permeability values for these gases being 0.90 cm3 mm m−2 day−1 kPa− and 0.26 cm3 mm m−2 day−1 kPa, respectively, when the films were cast without the enzymatic treatment, but decreasing to 0.14 ± 0.02 cm3 mm m−2 day−1 kPa (CO2) and 0.02 ± 0.02 cm3 mm m−2 day−1 kPa (O2) in the presence of 24 U/g of mTG. These novel materials, prepared from renewable sources, could potentially be used in the food packaging field to replace/reduce the highly pollutant petroleum-based ones.