Abstract Purpose Coffee is an important source of bioactive compounds, including caffeine, trigonelline, and phenolic compounds. Several studies have highlighted the preventive effects of coffee consumption on major cardiometabolic (CM) diseases, but the impact of different coffee dosages on markers of CM risk in a real-life setting has not been fully understood. This study aimed to investigate the effect of coffee and cocoa-based confectionery containing coffee consumption on several CM risk factors in healthy subjects. Methods In a three-arm, crossover, randomized trial, 21 volunteers were assigned to consume in a random order for 1 month: 1 cup of espresso coffee/day, 3 cups of espresso coffee/day, and 1 cup of espresso coffee plus 2 cocoa-based products containing coffee, twice per day. At the last day of each treatment, blood samples were collected and used for the analysis of inflammatory markers, trimethylamine N-oxide, nitric oxide, blood lipids, and markers of glucose/insulin metabolism. Moreover, anthropometric parameters and blood pressure were measured. Finally, food consumption during the interventions was monitored. Results After 1 month, energy intake did not change among treatments, while significant differences were observed in the intake of saturated fatty acids, sugars, and total carbohydrates. No significant effect on CM markers was observed following neither the consumption of different coffee dosages nor after cocoa-based products containing coffee. Conclusions The daily consumption of common dosages of coffee and its substitution with cocoa-based products containing coffee showed no effect on CM risk factors in healthy subjects. Trial registration number Registered at clinicaltrials.gov as NCT03166540, May 21, 2017.