A nitrogen-flush scrubber system for a controlled atmosphere room in which the amount of nitrogen required to flush the regenerated scrubber beds is significantly reduced. The present invention provides a dual-bed scrubber system in which low oxygen air salvaged from the active scrubber bed is used to flush high oxygen air from the regenerated scrubber bed prior to nitrogen flush. The scrubber system may include two scrubber beds that are used alternately to scrub air from the CA room. One scrubber bed is used as an active scrubber bed to remove carbon dioxide from the air. The inactive scrubber bed may be regenerated while it is inactive. When the active scrubber bed becomes sufficiently saturated, the control system may switch the active scrubber bed, using the regenerated bed as the active scrubber bed and allowing the saturated bed to be regenerated.