Very little is known about the effects of an organic or conventional diet on animal physiology and health. Here, we report the effect of contrasting crop protection (with or without chemosynthetic pesticides) and fertilization (manure or mineral fertilizers) regimes on feed composition and growth and the physiological parameters of rats. The use of manure instead of mineral fertilizers in feed production resulted in lower concentrations of protein (18.8 vs 20.6%) and cadmium (3.33 vs 4.92 μg/100 g) but higher concentrations of polyphenols (1.46 vs 0.89 g/100 g) in feeds and higher body protein (22.0 vs 21.5%), body ash (3.59 vs 3.51%), white blood cell count (10.86 vs 8.19 × 10³/mm³), plasma glucose (7.23 vs 6.22 mmol/L), leptin (3.56 vs 2.78 ng/mL), insulin-like growth factor 1 (1.87 vs 1.28 μg/mL), corticosterone (247 vs 209 ng/mL), and spontaneous lymphocyte proliferation (11.14 vs 5.03 × 10³ cpm) but lower plasma testosterone (1.07 vs 1.97 ng/mL) and mitogen stimulated proliferation of lymphocytes (182 vs 278 × 10³ cpm) in rats. There were no main effects of crop protection, but a range of significant interactions between fertilization and crop protection occurred.