The former Celtic captain joined the club from Middlesbrough last summer on a one-year deal which included the option of an added 12 months, but McManus has extended his stay further still.
The 31-year-old was a key player in Motherwell's Scottish Premiership campaign, which culminated in a 1-0 win at Pittodrie to snatch second place.
McManus told the club's official website: "Last season couldn't have gone any better for me personally.
"I wanted to come here at the start of last season, play as many games as possible and, hopefully, bring something to the team.
"I've really enjoyed it and the decision to extend really was a no-brainer."
Manager Stuart McCall added: "On the pitch, Stephen is a rock for us at the heart of the defence as well as a real influence in the dressing room and around the club.
"He played more than anyone at the club last season, missing just one game, so we're thrilled he has extended his stay.
"We hope to be in a position to confirm new deals for other players in the very near future too, with preparations for next season already well under way."