No, the smell doesn't stay in the super, or on the frames, nor does it in any way contaminate the honey. That is, if you use the fume boards and don't squirt it directly on the frame top bars as I saw one lame brain do. You really need more than one squirt to make the boards work effectively though. We run a stream back and forth across the board several times. Not much fun standing around watching the grass grow while waiting for the fumes to work. Also, if you haven't done so, paint the fume boards black; they work much better.