Brought up as a youth within the Ambri-Piotta club, Pestoni was re-signed to a further two-year contract extension on February 27, 2012, to remain under contract with Ambri until 2016. In December 2013, Pestoni was loaned to Genève-Servette HC for the 2013 Spengler Cup, which he would eventually win. He played a huge role in the title, tallying 4 points in 4 games. He was again loaned to the reigning champion for the 2014 edition and scored 3 goals to lead Geneva to its second title. He was also named to the tournament All-Star Team. After 8 seasons and 330 games with Ambri-Piotta, Pestoni agreed to a three-year contract with the ZSC Lions. On October 5, 2016, the ZSC Lions announced that Pestoni would be suspended for five weeks due to poor physical conditions. During that span, he'll have to participate in an intensive off-ice training in order to lose weight and increase his fitness level. Pestoni eventually returned to game action on November 11, 2016, against his former team, HC Ambrì-Piotta, at the Valascia. The day after that, on November 12, 2016, Pestoni scored his first goal since his return. In April 2018, Pestoni won the Swiss championship with the Lions, appearing in only 6 postseason games and scoring no point. On May 23, 2018, the ZSC Lions announced that Pestoni would no longer be playing for the team -despite one year remaining on his contract- and that he could either find a new team or report to their affiliate, the GCK Lions of the Swiss League. Should he fail to sign a contract with a new organization, he would still be paid the remaining CHF 750,000 on his contract. Pestoni played 84 regular season games with Zurich as well as 12 postseason contests over 2 seasons. On June 5, 2018, Pestoni signed a one-year contract worth CHF 500,000 with HC Davos for the 2018–19 season with an option for the following season. Pestoni made his return to the Swiss national team while playing for Davos, appearing in two games at the Lucern Cup in December. On January 4, 2019, Pestoni decided to forgo his option with Davos by signing a two-year deal worth CHF 1.2 million with SC Bern beginning in the 2019–20 season.
Personal life
Pestoni is a huge soccer fan and roots for both the Swiss national team and AC Milan. On January 8, 2017, Pestoni missed his team's afternoon game as his girlfriend Carolina gave birth to the couple's first child.