Purpose: Studies on the effect of body weight and coffee consumption on leptin, vitamin B12, and folic acid are scarce and conflicting. This study investigates the effect of body weight and/or coffee consumption rate on the serum levels of these molecules in healthy young adult males. Patients and Methods: This observational cross-sectional study was carried out at the faculty of pharmacy, Applied Science Private University (ASU), Amman, Jordan, from July to September 2020. Young healthy males were invited to participate in the study and fill a questionnaire regarding lifestyle habits including coffee consumption during the last 3 months, medical history, and anthropometric measurements. Depending on BMI and extent of coffee consumption, participants were divided into 4 groups; normal body weight and moderate coffee consumption (NW/MCC) group; normal body weight and heavy coffee consumption (NW/HCC) group; overweight and moderate coffee consumption (OW/MCC) group; overweight and heavy coffee consumption (OW/HCC) group. Serum samples were taken to measure leptin, vitamin B12, and folic acid levels in addition to morning and midnight salivary cortisol and dehydroepiandrosterone (DHEA) samples. Results: Healthy males (n = 122) aged 18 to 26 years continued participation in this study. Serum levels of leptin in NW/MCC, NW/HCC, OW/MCC, OW/HCC groups were 5.93, 5.75, 14.86, 16.79 ng/mL, respectively. Serum levels of vitamin B12 in these groups were 356.09, 402.71, 334.25, 331.05 pg/mL, respectively. While, the serum levels of folic acid were 8.92, 10.27, 10.12, 10.47 ng/mL, respectively. Body weight was positively associated with leptin (p = 0.00), negatively associated with vitamin B12 (p = 0.047), and not associated with folic acid (p = 0.235). Coffee consumption rate had no significant effect on leptin, vitamin B12, or folic acid. Finally, the combination of body weight and coffee consumption had no significant effect on leptin, vitamin B12, or folic acid. Conclusion: There was no possible synergistic effect between body weight and coffee consumption rate on leptin, vitamin B12, or folic acid levels. However, overweight was associated with higher leptin, lower vitamin B12, and no change in folic acid levels. Trial Registration: This trial was registered at clinicaltrials.gov as NCT04488731.