A method of operating a two-stroke cycle, opposed-piston engine comprising a pumping device coupled to pump air to cylinders of the engine through a charge air cooler and an aftertreatment system of thermally-activated devices coupled to receive exhaust from the cylinders by which a thermal state of the exhaust sufficient to sustain thermal activation of one or more of the aftertreatment system devices may be maintained during a deceleration or motoring condition of operation by reducing the mass airflow to the engine.