This study was conducted to investigate the effects of zinc (Zn), as a combination of oxide (ZnO) and sulfate (ZnSO4), compared with incremental levels of zinc hydroxychloride (ZH) on tibia traits, intestinal integrity, expression of selected jejunal genes, cecal short chain fatty acids and microbial composition in broilers. Day-old male Ross 308 chicks (n = 784) were randomly allocated to seven dietary treatments, each replicated seven times with 16 chicks per replication. The dietary treatments included a negative control diet (NC) with no supplemental Zn, a positive control (PC) with 100 mg/kg supplemental Zn from an ionic bound source combination (50 mg/kg ZnO + 50 mg/kg ZnSO4), and the NC diet supplemented with one of 20, 40, 60, 80, or 100 mg/kg Zn as ZH. The diets were fed over starter (1–14 d) and grower (14–35 d) phases, with tissue and digesta samples collected from 3 birds per replicate on days 14 and 35. The results showed that dietary Zn level had a significant effect on tibia breaking strength on d 35 (P < 0.05), and tibia Zn concentration both on d 14 and d 35 (P < 0.01). Dietary Zn levels linearly (P < 0.01) increased cecal lactic acid production, increased Lactobacillus, and decreased Bacillus and total bacteria counts (P < 0.05). Inclusion of 80 and 100 mg/kg Zn as ZH tended to upregulate the expression of claudin-1 (P = 0.088) and tight junction protein-1 (P = 0.086). The results obtained in this study suggest that a non-Zn supplemented diet can negatively influence tibia development and gut microbiota composition in broiler chickens. Higher supplemental Zn in the diet alters cecal microbiota population in favor of Lactobacillus and can decrease the total bacterial load. Supplemental Zn level in the feed have the potential to manipulate the jejunal gut integrity at a molecular level.