A whey protein isolate solution was heat-denatured and treated with the enzyme transglutaminase which cross-linked ≈26% of the amino groups and increased the magnitude of ζ-potential value. The protein solution was microemulsified and then the resulting water-in-oil microemulsion was dispersed within a gallic acid-rich model wastewater. Gallic acid extraction by the outlined microemulsion liquid membrane (MLM) from the exterior aqueous phase (wastewater) and accumulation within the internal aqueous nanodroplets induced proteins cold-set gelation and resulted in formation of gallic acid-enveloping nanoparticles. Measurements with a strain-controlled rheometer indicated a progressive increase in the MLM viscosity during gallic acid recovery corresponding to particles formation. The mean hydrodynamic size of the nanoparticles made from the heat-denatured and pre-heated enzymatically cross-linked proteins was 137 and 122 nm, respectively. The enzymatic cross-linking of whey proteins lead to a higher gallic acid recovery yield and increased the glass transition enthalpy and temperature. A similar impact on glass transition indices was observed by the gallic acid-induced nanoparticulation of proteins. Scanning electron microscopy showed existence of numerous jammed/fused nanoparticles. It was suggested based on the results of Fourier transform infra-red spectroscopy that the in situ nanoparticulation of proteins shifted the C−N stretching and C−H bending peaks to higher wavenumbers. X-ray diffraction results proposed a decreased β-sheet content for proteins because of the acid-induced particulation. The nanoparticles made from the enzymatically cross-linked protein were more stable against the in vitro gastrointestinal digestion and retained almost 19% of the entrapped gallic acid after 300 min sequential gastric and intestinal digestions