Under new coach Martin Jol, Vertonghen retained his place in the starting line-up for the 2009–10 season.
Despite injuring his toe while on international duty against Spain the previous week, he scored his first goal of the season, a free kick, in a 6–0 thrashing of NAC Breda on 13 September.
With the departure of Thomas Vermaelen to Arsenal, he and fellow Belgian Toby Alderweireld become the first choice centre-back pairing and soon became a firm fans' favourite.
Despite Ajax's erratic form in the latter weeks leading up to the winter break, he turned in some strong performances and attracted the interest of a number of clubs, including Barcelona, but he played down the rumours, stating his intent to at least see out his contract with Ajax.

After the winter break, Ajax went on a nine-game unbeaten streak in the league, with Vertonghen playing a key role.
Their run of six consecutive clean sheets was ended in a 4–1 home win over PSV when the visiting side were awarded a penalty.
Vertonghen was linked with a move to Newcastle United, and later he was also linked with Milan, stating, "I've heard Milan Director Adriano Galliani talk about me after the Champions League match in San Siro and his words were very flattering."

Vertonghen stated on numerous occasions late in the 2010–11 season that he was considering leaving Ajax at the end of that season.
In May 2011, Frank de Boer confirmed Manchester City boss Roberto Mancini was present at the 2011 KNVB Cup Final held on 7 May 2011, where Vertonghen's side lost 3–2 to Twente.
Mancini was reportedly scouting Vertonghen to strengthen his side after they had qualified for the UEFA Champions League 2011–12 campaign.
Under new coach Martin Jol, Vertonghen retained his place in the starting line-up for the 2009–10 season. Despite injuring his toe while on international duty against Spain the previous week, he scored his first goal of the season, a free kick, in a 6–0 thrashing of NAC Breda on 13 September. With the departure of Thomas Vermaelen to Arsenal, he and fellow Belgian Toby Alderweireld become the first choice centre-back pairing and soon became a firm fans' favourite. Despite Ajax's erratic form in the latter weeks leading up to the winter break, he turned in some strong performances and attracted the interest of a number of clubs, including Barcelona, but he played down the rumours, stating his intent to at least see out his contract with Ajax.
After the winter break, Ajax went on a nine-game unbeaten streak in the league, with Vertonghen playing a key role. Their run of six consecutive clean sheets was ended in a 4–1 home win over PSV when the visiting side were awarded a penalty. Vertonghen was linked with a move to Newcastle United, and later he was also linked with Milan, stating, "I've heard Milan Director Adriano Galliani talk about me after the Champions League match in San Siro and his words were very flattering."
Vertonghen stated on numerous occasions late in the 2010–11 season that he was considering leaving Ajax at the end of that season. In May 2011, Frank de Boer confirmed Manchester City boss Roberto Mancini was present at the 2011 KNVB Cup Final held on 7 May 2011, where Vertonghen's side lost 3–2 to Twente. Mancini was reportedly scouting Vertonghen to strengthen his side after they had qualified for the UEFA Champions League 2011–12 campaign.
Jan Vertonghen