The aim of this meta-analysis was to compare the effects of endurance, strength, and combined training on inflammatory markers and adipokine concentrations in overweight and obese adults. We performed a literature search of the Cochrane Library, PubMed, Scopus, and Web of Science databases and identified 24 randomised control trials published prior to June 2021. Our findings indicate that endurance training was significantly more beneficial than strength training in reducing C-reactive protein (CRP) (standard mean difference (SMD): −1.317, 95% confidence intervals (CI): −2.565, −0.070, p = 0.0385), interleukin 6 (IL-6) (SMD: −0.363, 95% CI: −0.648, −0.078, p = 0.0126), and visfatin (SMD: −0.618, 95% CI: −1.015, −0.222, p = 0.0023) concentrations. Moreover, combined training was more beneficial than strength training alone in lowering tumour necrosis factor-alpha (TNF-α) levels (SMD: 0.890, 95% CI: −0.301, 1.478, p = 0.0030). There were no differences between the effects of different types of training programmes on adiponectin and leptin concentrations. In conclusion, compared with strength training, endurance training is more effective in lowering CRP, IL-6, and visfatin concentrations, while combined training is more beneficial in reducing TNF-α levels in overweight and obese adults. Further studies are needed to determine which type of training has a better effect on adiponectin and leptin concentrations in this population.