The 40-year-old Glaswegian joins the club after the departure of Dougie White and Stewart Murray, bringing with him a strong footballing pedigree, and a wealth of experience, including over 170 pro appearances for Dumbarton.
He said: “I feel that I’m inheriting a strong team with potential, where the foundations have been built, and we just need to get over the hurdle of semi-finals.
“In terms of the league, there’s some strong teams in there. It might take some time to work towards the top two spots, but it’s something to aim towards.”
Discussing areas for improvement and potential transfer targetse, the new boss said: “I’m looking at boys I’ve worked with that I’d like to bring in, who could bring something to any team in the league.
“We want players that can bring quality and experience all round, because we want to be contenders.”
Flannery’s first match in charge is on Monday, following the Tweedie Cup match away to Nithsdale Wanderers on Saturday.
* Having played at both junior and professional level, Flannery’s pro career saw him scoring over 70 goals for The Sons.
He also had spells at other clubs such as Greenock Morton, Stenhousemuir, Livingstone and Bury.
Since then, Flannery has been co-manager at Cambuslang Rangers, before more recently taking on a coaching role at Gretna 2008, his last club before taking the reins at Mids.