More than 120 members of the Prospect union began the 48-hour strike at midday on Tuesday. They have now begun working to rule.
Highlands and Islands Airports Limited (Hial) and Prospect are in dispute over an increase in wages for workers.
Ten of the airports remained open during the strike.
Scottish government-owned Hial gave managers training in security work to keep sites on the Hebrides and Northern Isles and at Inverness, Campbeltown and Wick open.
Dundee was temporarily shut.
Industrial action by security staff at Scotland's 11 regional airports has come to an end without a resolution to the dispute over pay and conditions.