Šimundža began his coaching career at his hometown club Železničar Maribor, where he was coaching youth selections. He started his senior coaching career in 2007, when he was appointed as an assistant coach of Pavel Pinni at Celje. In 2008, he became an assistant of Darko Milanič at Maribor. He was part of Maribor's sports department until 2011 when he was selected as a head coach of Mura 05. His season with Mura 05 was impressive and he turned the team around, changing it from a relegation contender to the eventual UEFA competitions qualifier, as the club finished third during the 2011–12 Slovenian PrvaLiga season. By the end of his first season as head coach, he was nominated for the best coach in the league. He then accepted an offer from Austrian side GAK, signing with the club in June 2012. However, the club went bankrupt a few months later and Šimundža returned to Mura 05 in early 2013. After the 2012–13 season, Mura 05 also went bankrupt, and Šimundža took over the Slovenian Second League side Aluminij in June 2013.