We studied rheology and nanostructures (by Small Angle Neutron Scattering) of heat-set canola seed protein gels, containing cruciferin and napin, prepared at pH 8 and pH 11. We focused on gastric and intestinal digestion of 10 mm pieces, mimicking human gastro-intestinal tract. Stronger gels, prepared at pH 11 (above the isoelectric points (IEP), of both proteins), retained local folded and compact conformations, close to native ones. Preparation at pH 8 (below napin's IEP but above cruciferin's one), could destabilize conformations due to charge differences of the proteins. For preparation pH 8, proteins were almost unfolded, and the gel softer. In gastric digestion, modulus decreased for pH 8 gels, but surprisingly, increased for pH 11. We propose a competition between unfolding, increasing local interactions (hence the modulus), and enzymatic scission. Scission could be less efficient for pH 11 gels, with less unfolded proteins and higher crosslink density, hindering enzymatic diffusion. Additional interactions could result from crossing one or two IEPs, towards gastric pH 2. For intestinal digestion, the two gels behave similar (proteins re-compaction and modulus decrease). Beyond loss of submicronic connectivity, external erosion of the gel for largest times is observed, but less on SANS, which involves the center of the piece.