He was appointed head coach of Finland's national team in 2014. In April 2016, he was named head coach of SC Bern of the Swiss top-flight National League A (NLA). He guided the Finnish national team to a silver medal at the 2016 IIHF World Championships in Russia before stepping aside to take on the Bern job. He guided Bern to the Swiss championship in his first year in charge (2017) and also in 2019. On January 28, 2020, Jalonen was fired by SC Bern, following bad results. Hans Kossmann took over at the helm of the team. Bern was ranked 9th in the Swiss championship when Jalonen was sacked.