Transglutaminase is often used to improve functional properties of plant proteins. Here, we report on the effects of the fractionation procedure on transglutaminase susceptibility of mung bean proteins at three length scales: molecular, colloidal and bulk. Dispersions of 4 wt% mung bean protein fractions were treated with transglutaminase. The four fractions were obtained through (1) dry fractionation (fine fraction); (2) dry fractionation with additional heating; (3) lab-scale wet fractionation; and (4) a commercial protein isolate. Analysis of rheological properties (at 9.5 wt% dry matter) revealed that transglutaminase crosslinking formed tougher materials when using the fine fraction, the heated fine fraction, and the wet fractionated isolate, while the rheological properties of the protein isolate were hardly changed. Proteins in all fractions were crosslinked by transglutaminase at molecular scale, as confirmed by an increase in large molecular weight bands in gel electrophoresis, but the extent of crosslinking depended on the fraction used. The molecular changes also resulted in altered physical chemical properties for some fractions, as revealed by protein dispersibility, confocal laser scanning microscopy, and particle size distribution. At the colloidal scale, transglutaminase crosslinking led to an increased particle size in the fine fraction and heated fine fraction, while particle sizes of the wet fractionated isolate and commercial protein isolate were mostly unaffected. The differences between the fractions were explained by three mechanistic crosslinking routes. To conclude, protein fractionation procedure greatly affected susceptibility to transglutaminase.