Purpose Obstructive sleep apnea (OSA) is highly prevalent but mostly undiagnosed in obese patients scheduled for bariatric surgery. To prevent cardiopulmonary complications, many clinics perform preoperative OSA screening. Consequently, adequate adherence to continuous positive airway pressure (CPAP) therapy is essential but challenging. We aimed to evaluate CPAP adherence and its influence on postoperative outcomes. Methods In a prospective multicenter cohort study, we compared different perioperative strategies for handling undiagnosed OSA in bariatric patients. In this subgroup analysis, patients newly diagnosed with OSA were compared to those with pre-existing OSA. We assessed inadequate CPAP adherence, defined as < 4 h/night, between the preoperative period and 6 months postoperative. Cardiopulmonary complications and (un)scheduled ICU admissions were also evaluated. Results In total, 272 patients with newly diagnosed OSA (67.4%) and 132 patients with pre-existing OSA (32.6%) were included. Before surgery, 41 newly diagnosed patients used CPAP inadequately, compared to 5 patients with pre-existing OSA (15% vs. 4%, p = 0.049). Six months after surgery, inadequate CPAP use increased to 73% for newly diagnosed patients and 39% for patients with pre-existing OSA, respectively ( p < 0.001). Incidences of cardiopulmonary complications, scheduled, and unscheduled ICU admissions were similar in the two study groups ( p = 0.600, p = 0.972, and p = 0.980, respectively). Conclusion Inadequate CPAP adherence is higher in bariatric patients newly diagnosed with OSA when compared to patients with pre-existing OSA. Strategies to increase CPAP adherence may be valuable when considering routine OSA screening and CPAP therapy in patients undergoing bariatric surgery. Further studies are needed to improve current guidelines on perioperative OSA management of obese patients. Trial registration POPCORN study, registered at Netherlands Trial Register, https://www.trialregister.nl/trial/6805 . ID no: 6805.