Epidemiological studies have shown an inverse association between coffee consumption and risk of type 2 diabetes. However, the randomized controlled trials in prediabetes are limited to evaluate the effects of coffee. The purpose of this study is to investigate the effects of coffee on metabolic factors and inflammation in individuals with prediabetes and obesity. A double-blind, randomized controlled trial is designed to explore the effects of coffee consumption on participants with prediabetes and obesity. A total of 100 eligible participants with prediabetes and obesity will be recruited from the Health Management Center of Nanjing First Hospital. These participants are randomly assigned in a 1:1 ratio to either the coffee capsule group or the control group. The coffee capsule group will be instructed to consume 3.6 g of coffee capsules per day (0.3 g per capsule, 6 capsules per serving, twice a day, once in the morning and once in the middle of the day). The control group will be asked to consume 3.6 g of cornstarch capsules (0.3 g per capsule, 6 capsules per serving, twice a day, once in the morning and once in the middle of the day). 75 g oral glucose tolerance test, 2-week blinded continuous glucose measurement and others will be performed before and after the 3-month intervention. During the three months of intervention, the information on dietary intake, physical activity and sleep of participants will be systematically collected. To comprehensively assess the impact of coffee intake on prediabetes and obesity, we will analyze the effects of coffee capsules on various metabolic and inflammatory markers, including glucose metabolism, lipid profiles, blood pressure, adiponectin, high sensitivity C-reactive protein, interleukin-6, body mass index, body composition, the degree of hepatic steatosis and so on. We will further adjust for potential confounding factors such as lifestyle factors to better understand the underlying biological mechanisms driving this association.