This study aimed to evaluate the effect of increasing levels of red propolis extract (RPE) in the diet of confined sheep on performance and histomorphometric parameters of rumen and intestine and histopathological parameters of liver and kidney. Thirty-five male sheep (17.08 ± 2.36 kg) were used, distributed in a completely randomized design, with five treatments (0, 7, 14, 21, and 28 mL day− 1 RPE) and seven replications, submitted to one 68-day trial period. At the end of the experimental period, the animals were slaughtered, and, rumen, intestine, liver, and kidney samples were collected (histomorphometry and histopathology). The dry matter intake (DMI), total weight gain (TWG), epithelial thickness ruminal (ETR), a keratinized portion of the epithelium ruminal (KER), a non-keratinized portion of the epithelium ruminal (NKP), papilla height (PH), papilla width (PW), mucosal thickness (MT) and submucosal thickness (ST) exhibited quadratic curve behavior (P < 0.05) with the inclusion of RPE. In addition, the highest level of 28 mL day− 1 RPE resulted in a 20.24% increase in TWG compared to the control group. Therefore, the 28 mL day-1 RPE level is indicated as a natural additive more significant to provide greater absorptive areas of the rumen and intestine, and an increase in total weight gain.