Gastroesophageal Reflux Disease (GERD) is multifactorial pathogenesis characterized by the abnormal reflux of stomach contents into the esophagus. Symptoms are worse after the ingestion of certain foods, such as coffee. Hence, a randomized pilot study conducted on 40 Italian subjects was assessed to verify the effect of standard (SC) and dewaxed coffee (DC) consumption on gastroesophageal reflux symptoms and quality of life in patients with gastrointestinal diseases. The assessment of patient diaries highlighted a significant percentage reduction of symptoms frequency when consuming DC and a significant increase in both heartburn-free and regurgitation-free days. Consequentially, patients had a significant increase of antacid-free days during the DC assumption. Moreover, the polyphenolic profile of coffee pods was ascertained through UHPLC-Q-Orbitrap HRMS analysis. Chlorogenic acids (CGAs) were the most abundant investigated compounds with a concentration level ranging between 7.316 (DC) and 6.721 mg/g (SC). Apart from CGAs, caffeine was quantified at a concentration level of 5.691 mg/g and 11.091 for DC and SC, respectively. While still preliminary, data obtained from the present pilot study provide promising evidence for the efficacy of DC consumption in patients with GERD. Therefore, this treatment might represent a feasible way to make coffee more digestible and better tolerated.