The present disclosure pertains to a ventilation therapy system configured to control a pressure or flow generator to apply an intra-pulmonary percussive ventilation therapy regime to a pressurized flow of breathable gas during baseline ventilation therapy. The ventilation therapy system is configured to automatically control the pressurized flow of breathable gas. The system may automatically control an extent of hyperinflation during IPPV in a subject. The system is configured such that therapy set points, alarm settings, and/or other factors are automatically adjusted during the application of IPPV relative to the set points and alarm settings during baseline ventilation therapy. In some embodiments, the system comprises one or more of a pressure or flow generator, a subject interface, one or more sensors, one or more processors, a user interface, electronic storage, and/or other components.