Evidence of the role of cooking methods on inflammation and metabolic health is scarce due to the paucity of large-size studies. Our aim was to evaluate the association of cooking methods with inflammatory markers, renal function, and other hormones and nutritional biomarkers in a general population of older adults. In a cross sectional analysis with 2467 individuals aged ≥ 65, dietary and cooking information was collected using a validated face-to-face dietary history. Eight cooking methods were considered: raw, boiling, roasting, pan-frying, frying, toasting, sautéing, and stewing. Biomarkers were analyzed in a central laboratory following standard procedures. Marginal effects from generalized linear models were calculated and percentage differences (PD) of the multivariable-adjusted means of biomarkers between extreme sex-specific quintiles (Q) of cooking methods consumption were computed ([Q5 − Q1/Q1] × 100). Participants’ mean age was 71.6 years (53% women). Significant PD for the highest vs lowest quintile of raw food consumption was − 54.7% for high sensitivity-C reactive protein (hs-CRP), − 11.9% for neutrophils, − 11.9% for Growth Differentiation Factor-15, − 25.0% for Interleukin-6 (IL-6), − 12.3% for urinary albumin, and − 10.3% for uric acid. PD for boiling were − 17.8% for hs-CRP, − 12.4% for urinary albumin, and − 11.3% for thyroid-stimulating hormone. Concerning pan-frying, the PD was − 23.2% for hs-CRP, − 11.5% for IL-6, − 16.3% for urinary albumin and 10.9% for serum vitamin D. For frying, the PD was a 25.7% for hs-CRP, and − 12.6% for vitamin D. For toasting, corresponding figures were − 21.4% for hs-CRP, − 11.1% for IL-6 and 10.6% for vitamin D. For stewing, the PD was 13.3% for hs-CRP. Raw, boiling, pan-frying, and toasting were associated with healthy profiles as for inflammatory markers, renal function, thyroid hormones, and serum vitamin D. On the contrary, frying and, to a less extent, stewing showed unhealthier profiles. Cooking methods not including added fats where healthier than those with added fats heated at high temperatures or during longer periods of time.