The incident took place at Lamb Holm Airfield in Orkney on May 9 at 12.30pm and has now been published in an Air Accidents Investigation Branch report.
It was the first time the pilot had been in charge of the aircraft and his only time operating it from the left seat.
The report says when touching down he was trying to keep the microlight straight by pressing down on the right rudder bar.
It appeared to him this was ineffective so he pushed harder, without realising his foot had slipped on to the left bar for a pilot in the right-hand seat.
The aircraft veered sharply off the runway and hit a fence at low speed.
Damage was done to the propeller, nose landing gear and floor panel.
There was one passenger on board and the pilot was the only crew member. No one was injured.
Meanwhile, another incident in the report saw a pilot damage an aircraft by flying it into concrete on a grass runway on Mull.
The left mainwheel struck the runway designator numbers at Glenforsa Airport.
After aborting the landing, the flight was diverted to Oban Airport and a full emergency was called by the pilot.
The left landing gear collapsed on touchdown and it veered off the runway.
There were two passengers on board and the pilot was the only crew member. No one was injured.
The incident took place at 3.30pm on May 12.
Damage to the left landing gear and left wing landing light were recorded in the report.
The pilot said in future he would ensure that his touchdown aiming point allowed more clearance beyond concrete numbers, while the airport operator said it will review information published on its website.