The most effective type of training to improve cardiometabolic parameters in overweight subjects is unknown. This meta-analysis compared the effect of endurance, strength and combined training on glucose, insulin metabolism and the lipid profile of overweight and obese adults. The Cochrane, PubMed, Scopus and Web of Science databases were searched to identify randomised trials assessing the effect of training intervention on fasting and 2 h glucose and insulin levels, glycated haemoglobin (HbA1c), homeostatic model assessment of insulin resistance (HOMA), C-peptide, total cholesterol (TC), low- (LDL-C) and high-density lipoprotein cholesterol and triglycerides (TG). Forty-six studies were included showing that endurance training more favourably reduced HbA1c (p = 0.044), and LDL-C (p = 0.021) than strength training. Endurance-strength training more effectively decreased glucose (p = 0.002), HbA1c (p = 0.032), HOMA (p = 0.002), TC (p = 0.039), LDL-C (p = 0.046), HDL (p = 0.036) and TG levels (p = 0.025) than strength training. Combined training significantly reduced the HOMA index (p = 0.009) and TG levels (p = 0.039) compared with endurance training. Endurance and endurance-strength training have a more favourable effect on glucose and insulin homeostasis and lipid profile than strength training in overweight and obese adults. However, the results from this meta-analysis should be interpreted cautiously due to significant heterogeneity among included studies.