The effect of calcium (Ca) on glycation markers is unknown. We hypothesized that increased Ca intake from skimmed milk associated with an energy-restricted diet intake will reduce glycation markers. This reduction will be associated with a greater improvement in markers of metabolic control in adults with type 2 diabetes, overweight, and low habitual Ca intake (<600 mg/d). In this secondary data analysis based on a crossover clinical trial, 14 adults were allocated into 2 groups: high calcium (shake containing 700 mg Ca/day) or low calcium (shake with 6.4 mg Ca/day), for 12 consecutive weeks per session. Energy-restricted diets were also prescribed (-500 kcal/d, 800 mg of dietary Ca/d) to all participants. Advanced glycation end products (AGEs), soluble receptor for AGEs (sRAGE), glycemic control, and lipid profile were assessed at baseline and after 12 weeks. High-calcium serum AGE concentrations and AGE/sRAGE ratio were lower at the end of the study. ΔAGE and ΔAGE/sRAGE ratio were both positively associated with Δtriglycerides, Δtotal cholesterol, Δtriglyceride-glucose index and variations, and Δvisceral adiposity index. ΔAGE/sRAGE was positively associated with Δfructosamine and Δhigh-density lipoprotein-cholesterol, and negatively associated with male sex. Consumption of approximately 1200 mg/day of calcium (3 servings of skim milk) reduced serum AGEs concentrations and the AGE/sRAGE ratio in individuals with diabetes. In general, positive changes in glycation markers are associated with lipid profile, insulin resistance, and adiposity markers worsening. ΔAGEs/ΔsRAGE ratio seems to be a better marker of metabolic status than ΔAGEs and ΔsRAGE alone. Registered in ClinicalTrials.gov (NCT02377076).