The effects of replacement of maize grain with ancient wheat by-products on intestinal morphometry and enzymatic activity in laying hens was studied. Eighty hens were divided into two groups (40 each, 8 replicates, 5 hens/replicate) fed two isoproteic and isoenergetic diets. In the treated group, part of the maize was replaced by a mix of ancient grains (AGs) middling, in a 50:50 ratio of Triticum aestivum L. var. spelta (spelt) and Triticum durum dicoccum L. (emmer wheat). The AG diet affected the weight of all the large intestine tracts, decreasing the weight of caeca (p < 0.01) and increasing those of colon (p < 0.01), rectum and cloaca (p < 0.05). Villus height in the AG group was higher (p < 0.01) than the control for the duodenum and jejunum, while for the ileum, the control group showed the highest values (p < 0.01). The submucosa thickness was higher (p < 0.01) in the control group for the duodenum and ileum, while the jejunum for the AG group showed the highest (p < 0.05) submucosa thickness. The crypts depth was higher (p < 0.01) in the control group for the duodenum and ileum. Enzyme activity was enhanced by AGs (p < 0.01) in the duodenum. Regarding the jejunum, sucrase-isomaltase and alkaline phosphatase had higher activity (p < 0.05 and p < 0.01, respectively) in the AG group. In the ileum, sucrase-isomaltase showed higher activity (p < 0.01) in the control group, while alkaline phosphatase showed the highest values (p < 0.05) in the AG group. Overall, results suggested that the dietary inclusion of AGs exerted positive effects in hens, showing an improved intestinal function.