Cowley will return to the club where he spent three seasons when Pompey visit Sincil Bank on Tuesday in a League One fixture.
Ahead of the fixture though, the Portsmouth manager took time to praise the work done by his Lincoln counterpart Appleton.
Cowley feels that on paper Lincoln were the best team in League One last season after having made some smart investments in the transfer market.
“They [Lincoln] have brilliant people at the wheel and Michael Appleton has done a brilliant job off the back of us being there”, Cowley said in an interview with The News.
“I think he’s a very good coach and I thought on paper last year they were the best team in the division and I think they deserve that accolade.
“Certainly the recruitment they did during the summer before last was just outstanding.
“In a year where there was a salary cap, maybe it was easier because everybody had similar finances, but they still worked tirelessly and made so many intelligent decisions, in my opinion.”
The way Lincoln City performed last year shows what can be achieved when a team’s foundations are right, the 43-year-old Portsmouth manager insists.
“When I looked at them on paper last year, I genuinely thought they were the best team in the division and credit it to them for that.
“It just shows what could be achieved if you get the foundations right.”
Lincoln and Portsmouth have similar records over the last nine League One games, with Appleton’s men collecting 13 points and Cowley’s side picking up 14 points.