This study tested the hypothesis that naturally and industrially produced trans fatty acids (TFA) exert distinct effects on rats’ metabolic parameters. Wistar rat groups were fed the diets: CONT - without added fat; HVF − 20% hydrogenated vegetable fat (HVF); and RUM − 20% ruminant fat. Biochemical markers, cytokine levels, fatty acid (FA) composition of liver, heart and adipose tissue, liver histology and the gut microbial composition were also evaluated. Rats fed RUM presented lower deposition of adipose tissue and LDL and higher HDL and anti-inflammatory IL-10 than those fed CONT and HVF. Pro-inflammatory cytokines, malondialdehyde (MDA) and aspartate aminotransferase (AST) were higher in group HVF than CONT and RUM. In all types of tissue, the highest TFA levels were observed in rats fed HVF, which contributed to the development of fatty liver. The RUM diet led to higher concentrations of stearic acid and conjugated linoleic acid (CLA). The lower incorporation of TFA and distinct FA profile in the liver of rats fed RUM compared to HVF could be associated with protection hepatic. The microbial gut communities were significantly dissimilar among the groups. It is plausible that ruminant fat might reduce risk parameters involved in the development of cardiovascular disease.