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 alongside two other recent signings, Jon Otsemobor and Danny Seaborne, 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.

After scoring seven league goals and helping Southampton gain promotion to the second level, Fonte was named 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, with Adam Lallana coming second with 18% and Dan Harding finishing third (7%).

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, playing the full 90 minutes in a 2–3 away loss against Manchester City.
He netted his first goal(s) in the competition in a 2–2 home draw to Fulham on 7 October, the second arriving in the last minute; on 24 August 2013, he scored a header in the 89th minute of the home game against Sunderland, rescuing a point for his team.

On 23 January 2014, Fonte was attacked by teammate Dani Osvaldo during a training session.
Subsequently, the latter was loaned out to Juventus F.C. during the winter transfer window.

On 8 August 2014, Fonte penned a new three-year deal with Southampton running until 2017, and was also named team captain.
He made his 250th league appearance for the club on 16 October 2016, in a 3–1 home win against Burnley.
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 alongside two other recent signings, Jon Otsemobor and Danny Seaborne, 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.
After scoring seven league goals and helping Southampton gain promotion to the second level, Fonte was named 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, with Adam Lallana coming second with 18% and Dan Harding finishing third (7%).
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, playing the full 90 minutes in a 2–3 away loss against Manchester City. He netted his first goal(s) in the competition in a 2–2 home draw to Fulham on 7 October, the second arriving in the last minute; on 24 August 2013, he scored a header in the 89th minute of the home game against Sunderland, rescuing a point for his team.
On 23 January 2014, Fonte was attacked by teammate Dani Osvaldo during a training session. Subsequently, the latter was loaned out to Juventus F.C. during the winter transfer window.
On 8 August 2014, Fonte penned a new three-year deal with Southampton running until 2017, and was also named team captain. He made his 250th league appearance for the club on 16 October 2016, in a 3–1 home win against Burnley.
José Fonte