This systematic review and meta-analysis aimed to evaluate the overall effect of caper fruit on the modulation of glycemic, lipid profile, liver enzymes, and body mass. Google Scholar, PubMed, and Scopus were explored to collect relevant studies in the last 10 years. RCTs with caper fruit supplementation or consumption in different cohorts of subjects with non-alcoholic fatty liver disease (NAFLD), Type-2-Diabetes (T2D), metabolic syndrome, and hyperlipidemia were included in this systematic review with a mean intervention duration from 2 to 12 weeks. The outcomes measured in this meta-analysis were liver enzymes such as aspartate aminotransferase (AST) and alanine aminotransferase (ALT), the lipid profile represented by triglycerides, total cholesterol (TC) with LDL and HDL and also, weight, and fasting blood glucose. Five randomized controlled trials, which involved a total of 178 adults, were included. According to the results, caper fruit seems to decrease liver enzymes ALT −12.29 U/L [−24.47, −0.11], AST −2.20 U/L [−4.70, 0.31]. Furthermore, the lipid profile seems to improve with a decrease in triglycerides. −11.89 mg/dL [−33.73, 9.95], LDL −4.80 mg/dL [−16.34, 6.74], HDL 0.72 mg/dL [0.10, 1.34], total cholesterol −7.83 mg/dL [−20.04, 4.38], FPG −17.93 [−42.66, 6.79], weight −1.00 kg [−1.44, −0.56]. Significant modulations were found only for ALT, HDL, and weight. In conclusion, this systematic review and meta-analysis showed the paucity of data available on the topic while showing the potential role of caper fruit as a promising food for improving the liver-lipid profile axis in patients with metabolic syndrome and diabetes. Further studies are required to confirm these results.