Glamorgan closed Day 1 on 25/4 after Middlesex recovered from 131/6 to post 384, thanks to Dawid Malan's 166.
Lukas Carey (4-54) and Michael Hogan (3-75) were the pick of the bowlers from Glamorgan's side but after Tom Helm's dramatic four-over spell, head coach Matt Maynard admitted his side wren't at their best with bat or ball.
"They could have been 130 for seven and you would have been looking at a different game," said Maynard. "There was a big momentum shift and Malan played a super knock well supported by Roland-Jones initially, then Sowter played some great shots.
"We didn't hold our bowling lengths particularly well all day, apart from Lukas Carey who had a great day with the ball.
"Then with nine overs to bat at the end, you can only lose, you can't gain anything.
From half an hour after lunch, it was probably our worst day of the season in the Championship but we've got three days to put that right."