Three valuable points took Cowden above the 10-man Gable Endies in the Ladbrokes League 2 table.
The Blue Brazil had been six starts without a win, but grabbed the lead on 19 minutes when striker Kris Renton was hauled down in the box by Michael Bolochoweckyj and Nikolay Todorov blasted the spot-kick past Allan Fleming.
Things got worse for Montrose after the half hour when Dundee United loanee Cammy Ballantyne was red-carded for a two-footed lunge at Craig Johnston.
Montrose struggled to bother the home skipper, keeper Dave McGurn, until the start of the second-half when Chris Templeman’s header came back off the woodwork.
The visitors’ task got even harder on 56 minutes when Kyle Miller’s cross was nodded across the face of the six-yard box and Renton dived to head home.
Cowdenbeath manager Liam Fox said: “Getting the first goal made a real difference and you could see the confidence level rise.
“It was good to build on a better performance at Berwick and we opened well, went ahead and then started to create a lot of good chances.
“You could feel in the dressing room after the game the difference in the atmosphere, but it is just three points and we have to look to keep building on that platform.”
Montrose boss Paul Hegarty felt his team paid for a slow start to the game, saying: “We came here with real confidence after our midweek win at Annan but we did not start playing until the half hour mark.
“By that time we were a goal down and then Cammy Ballantyne was red-carded, so while we came close with Chris Templeman’s effort which hit the wood, we did not really threaten Cowden enough.
“Another case of one step forward and two back for us.”