Manta was founded in 1998 after the purchase of the franchise rights from the defunct
Manta Sport. From 1999 to 2001, the club competed in the
Segunda Categoría, the third tier of
Ecuadorian football league system before being promoted in 2002 to
Serie B. Manta won promotion again in 2003 to
Serie A for the first time but finished poorly and were relegated back to Serie B where they would spend the next six seasons. 2009 saw the club back in Serie A but no titles were forthcoming and they were relegated again in 2014. They got promoted back to the Serie A in 2020 played in the first tier after a seven-year absence. After one season, they suffered another relegation, only returning to the top tier in 2024 after finishing second in the year's Serie B. ==Honours==