As the consumption of coffee beverages sometimes is reported to cause gastric irritation, for which an increased stomach acid secretion is one of the promoting factors, different processing technologies such as steam-treatment have been developed to reduce putative stomach irritating compounds. There is evidence-based data neither on the effect of detailed processing variations nor on individual coffee components affecting the proton secretory activity (PSA). This work aimed at developing a screening model suitable for investigating the effects of commercial coffee beverages and components thereof on human parietal cells. Human gastric cancer cells (HGT-1) were treated with reconstituted freeze-dried coffee beverages prepared from customary coffee products such as regular coffee (RC, n = 4), mild bean coffee (MBC, n = 5), stomach friendly coffee (SFC, n = 4), and SFC decaffeinated (SFCD, n = 3). PSA was analyzed by flow cytometry using the pH-sensitive dye SNARF-AM. Treatment of the cells with MBC did not result in a PSA different from RC treatment (p <or= 0.07), whereas cells treated with SFC (p <or= 0.04) or SFCD (p <or= 0.03) showed a significantly lower PSA than those treated with RC. Quantitative and principle component analysis of putative stomach irritating compounds revealed significantly reduced contents of (beta)N-alkanoyl-5-hydroxytryptamides, caffeine, N-methylpyridinium, and catechol in SFCD compared to RC. However, none of these compounds seem to act as the sole key bioactive reducing the PSA of SFCD, since their contents in MBC and SFC samples were not different from those in RC samples, although the PSA of these beverages was significantly lower than that of reconstituted freeze-dried RC beverage.