Metabolism of the nondigested fraction (NDF) from common bean ( Phaseolus vulgaris L.) by the human gut flora (hgf) produces short-chain fatty acids (SCFAs) that may benefit cancer by reducing colorectal tumor risks. This paper reports the effect of fermentation products (FP) by hgf (FP-hgf) from NDF of cooked beans on survival and protein expression associated with apoptosis, cell cycle arrest, and proliferation in human adenocarcinoma colon cancer cells. FP-hgf was the only inoculum eliciting butyrate production after 24 h of NDF fermentation using different bacterial sources. FP-hgf inhibited HT-29 cell growth and modulated protein expression associated with apoptosis, cell cycle arrest, and proliferation, as well as morphological changes linked to apoptosis evaluated by TUNEL and hematoxylin and eosin stains, confirming previous results on gene expression. The current results suggest that fermentation of NDF from common beans can elicit beneficial chemoprotective effects in colon cancer by modulating protein expression in HT-29 cells.