This study was designed to address key questions concerning the use of alternative protein sources for animal feeds and addresses aspects such as their nutrient composition and impact on gut function. We used casein (CAS), spray dried porcine plasma (SDPP), soybean meal (SBM), and yellow meal worm (YMW) as protein sources. We have investigated the use of intestinal organoids as a model to test the effects of different protein sources on the intestinal epithelium. Mouse enteroids were exposed to different undigested protein sources (4% w/v, viz. soybean meal, SBM; casein, CAS; spray dried plasma protein, SDPP; and yellow meal worm, YMW) or DMEM as a control. Microarrays were used to detail the global gene expression.