Joel Piroe's first-half strike was enough to secure a 1-0 victory over Huddersfield to end a run of four games without a win.
It was a fourth clean sheet in five games at home for Martin's men, who crucially found a breakthrough after failing to score in their previous two home matches.
Piroe's sixth goal of the season broke their goalscoring duck, but Martin singled out Downes for praise.
"Flynn was incredible, it's really difficult to single people out but he does the dirty work really well which sometimes goes unsung," he said.
"He enables people to do their roles brilliantly, he plays with no ego at all and knows exactly what his role in the team is and Kyle Naughton and the boys at the back appreciate him a lot - I know I would've if I'd had someone like Flynn playing in front of me.
"It's his willingness to learn, his attitude and attention to detail. He's playing a very different role to the one he played at his previous club as most of the guys are, but his willingness to learn, desire to win, his athleticism and improving technical ability is brilliant to see.
"For everyone the win is important. I have been so happy with performances, where they are going in terms of what we see with our eyes and what the performance data suggests - barring a 24-minute period at Luton really.
"The first half today was another step up, another improvement from where we have been. Now the challenge is to maintain that."
Despite the defeat, Huddersfield remain in seventh place, just three points off the play-off places.
"I feel we competed better in the second half than we did in the first," said Terriers manager Carlos Corberan.
"They had more clear chances, but they came from our mistakes. We didn't find a solution to the way they pressed and we lost organisation in defence for the goal they scored. Until that moment we were doing really well.
"We needed to manage our attack better the second half, we competed better and won more second balls.
"We played more in the offensive half and pressed well too. The mentality in the first half was not good enough.
"In some spaces of the pitch they were better individually than us which didn't allow us to counter attack. It's important to compete for 90 minutes.
"We have the intention to dominate the game with the ball but we need to find the balance of playing long and playing short."