Anti-nutritional factors such as trypsin inhibitors represent a major hindrance in the usage of soybean-based products as feed for non-ruminant feedstock. Here we studied the effect of four different methods of soybean processing to generate soybean meal (oil-extraction with a solvent, toasting, mechanical extraction, and fermentation) on the Kunitz trypsin inhibitor and soy protein. We visualized both proteins in situ using indirect immunofluorescence on resin sections with specific rabbit-raised polyclonal antibodies and laser-scanning confocal microscopy We characterized their cellular localization in raw soybeans and show that Kunitz trypsin inhibitor and soy protein occupy different domains related to protein globoids. Semi-quantification of the signal intensities showed an only moderate reduction in detectable Kunitz trypsin inhibitor epitopes after any type of processing. On the other hand, a considerable loss of trypsin inhibitor activity was shown with a standardized assay. The effect of toasting can be seen as significantly increased green fluorescence possibly due to the production of advanced glycosylation end products. This work introduces antibody-based in situ visualization as a new promising way to study anti-nutritional factors in soybean-derived products.