Wigan have announced Uwe Rosler as their new manager after agreeing compensation with Brentford.
Marseille have parted company with manager Elie Baup in the wake of Friday's defeat to Nantes at the Stade Velodrome.
The 27-year-old will link up with the Championship side as a free agent when his deal at Ashton Gate expires.
Skuse has played more than 300 games for his hometown club since his debut in 2005 but said the time had come for him to move on after they were relegated to League One.
"I loved my time at Bristol, they gave me a chance in the game and I'll always be grateful for that," Skuse told Town's official website.
"It's the right time for me to move on though. I need a fresh challenge and when I knew Ipswich wanted me, I didn't have to think too hard about the decision.
"I had a few options but with Mick McCarthy and Terry Connor in charge at Ipswich, that shows the intent of the club to move forward and I can't wait to get going."