Different studies have shown that milk may interact with polyphenols and affect their bioavailability in humans. The present study investigated the effect of the simultaneous consumption of coffee and milk on the urinary excretion of chlorogenic acids (CGA) and metabolites. Subjects were submitted to consumption of water, instant coffee (609 mmol of CGA) dissolved in water, and instant coffee dissolved in whole milk. Urine was collected for 24 h after consumption of each treatment for analysis of CGA and metabolites by HPLC/LC-MS. The amount of CGA and metabolites recovered after consumption of combined coffee-milk (40% ± 27%) was consistently lower in all subjects compared to that of coffee alone (68% ± 20%). Concluding, the simultaneous consumption of milk and coffee may impair the bioavailability of coffee CGA in humans.