Martignoni is from the Italian speaking Canton Ticino. He began his early career with local clubs US Gambarogno and ASC Gordola before moving on to FC Locarno in 2007. After a couple of years in the club's youth teams, he made a breakthrough into the first team in the latter part of 2009. Having featured sparingly, Martignoni went on loan for the 2010–2011 season to Italian club Cagliari Calcio, playing for the reserve team. Returning to Locarno at the end of the season, Martignoni has since established himself as a first choice defender in the team.
Martignoni was a Switzerland youth international. In 2009, he was part of the Swiss under-17 team that won the 2009 FIFA U-17 World Cup beating host nation Nigeria 1—0 in the final. Martignoni played in 6 of the 7 matches at the tournament and scored in the team's semi-final win against Colombia.