The use of natural feed additives could be a beneficial approach to maintaining the health of chickens and a way to improve food digestion. Flaxseed is a rich source of omega-3 fatty acid, alpha linolenic acid, oleic acid, and fiber. The purpose of this study was to evaluate the effects of dietary inclusion of 4% flaxseed on the intestinal morphology, specific enzymatic activity, and cecal microbiome in broiler chickens. The 4-week feeding trial was conducted on 100 Cobb 500 (14 days of age) unsexed broiler chickens divided into two groups: a control group (C) and an experimental group (E). The broilers were housed in boxes of size 3 m2 (each group was housed in a single box with 10 replicates, 5 chickens per replicate) and reared on permanent wood shaves litter (10–12 cm thick). At the end of the experiment, chickens (n = 10) were sacrificed and tissue samples were harvested from the duodenum, jejunum, and cecum for histological, enzymatic, and microbiome analyses. In group E, histological analysis revealed a significant increase in villus height (p < 0.001) possibly leading to enhanced intestinal nutrient absorption. An increase in the specific activities of α-amylase (p < 0.05), invertase (p < 0.01), and endo-β-1,4-glucanase (p < 0.001) was noticed in the E group for the duodenum and jejunum compared to the control group. In contrast, maltase activity decreased in the duodenum and increased in the jejunum in the E group. The trypsin and lipase specific activities did not vary in a significant way. In addition, the cecal microbiome of the E group was characterized by an increase in Lactobacilli (p < 0.01) and Clostridium coccoides and a decrease in Bacteroides, Ruminoccocus, Enterobacteriaceae, and Clostridium leptum. In conclusion, our results suggest that dietary supplementation of flaxseed meal may boost intestinal health status in poultry.