Fonte signed for Southampton on 9 January 2010 for a fee believed to be around the region of £1.2 million, signing a three-and-a-half-year contract. He made his debut one week later in a 1–1 draw at Millwall. His first goal for the Saints came on 28 August 2010, in a 4–0 away win against Bristol Rovers.
Fonte wasd in the League One Team of the Year for the 2010–11 season. He was also voted Southampton's Player of Year, achieving 64% of the overall vote.
On 29 December 2011, Fonte signed a new contract keeping him at the club until 2015. Southampton were top of the table when he signed, with the player having appeared in every league game, and he eventually contributed with 42 matches and one goal (against Coventry City in the final matchday) as the side achieved a second consecutive promotion.
Fonte made his debut in the Premier League on 19 August 2012. He netted his first Premier League goal(s) in a 2–2 home draw against Fulham on 7 October, the second arriving in the last mi