The nutritional quality of common wheat-based foods can be improved by adding flours from whole pulses or their carbohydrate and protein constituents. Faba bean (Vicia faba L.) is a pulse with high protein concentration. In this study, prepared faba bean (FB) flours were added to wheat based baked crackers. Wheat cracker recipes were modified by substituting forty percent wheat flour with flours from whole faba bean, starch enriched flour (starch 60%), protein concentrate (protein 60%) or protein isolate (protein 90%). Baked crackers were ground into meal and analyzed for their macronutrient composition, starch characteristics and in vitro starch hydrolysis. Faba bean supplemented crackers had lower (p ≤ 0.001) total starch concentrations, but proportionally higher protein (16.8–43%), dietary fiber (6.7–12.1%), fat (4.8–7.1%) and resistant starch (3.2–6%) (p ≤ 0.001) than wheat crackers (protein: 16.2%, dietary fiber: 6.3%, fat: 4.2, resistant starch: 1.2%). The increased amylose, amylopectin B1- chain and fat concentration from faba bean flour and starch flour supplementation in cracker recipe contributed to increased resistant starch. Flours from whole faba bean, starch or protein fractions improved the nutritional properties and functional value of the wheat-based crackers. The analytical analysis describing protein, starch composition and structure and in vitro enzymatic hydrolysis advance understanding of factors that account for the in vivo benefits of faba bean flours added to crackers in human physiological functions as also previously shown for pasta. The findings can be used to guide development of improve nutritional quality of similar wheat-based food products.