A system and a method for expiratory flow limitation (EFL) detection by controlling positive pressure (e.g., PEEP) applied during expiration for a subject is based on a temporary perturbation or adjustment of a pressure level of positive pressure during exhalation on selected breaths. The different responses to such a perturbation of flow-limited breaths compared to non-flow limited breaths is used to assess EFL in a subject. Automatic adjustments of the positive pressure applied to the patient are used in the disclosed algorithm to abolish EFL, and are implemented through existing ventilators and other respiratory devices.