Differentiation between organic and conventional coffee has increased due to the growing demand and high consumption of healthy foods that contain compounds with antioxidant potential, which have been associated with the reduction of chronic diseases. We used organic and conventional coffee in powder 4% (w/w) and infusions 5%, 10% and 20% (w/v) incorporated in a commercial diet to test in vivo. The levels of chlorogenic acid, caffeine and trigonelline were determined by high performance liquid chromatography. The body weight, weight gain, food consumption, aberrant foci crypt, mucin depleted foci, stress biomarkers protein carbonyl and malondialdehyde, biochemical parameters and behavior of the rats were compared between the experimental and control groups within a framework of colon carcinogenesis. The organic coffee showed higher levels of chlorogenic acid, caffeine and trigonelline than conventional, however, this difference did not significantly affect behavior. The infusions had an antioxidant effect, reducing the levels of malondialdehyde; however, the biochemical parameters of the serum were not altered, and there was neither induction nor prevention of preneoplasic lesions.