In January 2017 Machálek signed for MSFL side SK Líšeň, located on the outskirts of the South Moravian capital Brno. In the second half of the season, Machálek guided the club to avoid relegation and helping them finish 12th in the 2016–17 MSFL season. In the following season SK Líšeň surprisingly reached 3rd place in MSFL, with 16 points loss on the advancing team 1. SK Prostějov, Machálek's former club. Before 2018-19 MSFL season, Líšeň took advantage of cooperation with the second Brno club Zbrojovka and brought on loan Jakub Černín and Jakub Přichystal, who scored 13 goals in 15 games in the first half of 2018-19 MSFL season, meaning that Líšeň was half-season champion. Despite the fall in form in the second half of the season, Líšeň secured promotion to 2019–20 Czech National Football League for the first time in club history, thanks to 2-1 victory in the last round at FK Hodonín. In the premiere season in Czech 2. league, Líšeň presented with spontaneous and lively football under the guidance of Machálek and was the biggest surprise of the competition. He was determining offensive football tactics, mainly using 4–3–3 formation. After 11 rounds Líšeň had 13 points and reached 9th place in the competition. On 7 October 2019, rival team FC Zbrojovka Brno hired Machálek as their new coach, replacing Pavel Šustr. He led Zbrojovka for the first time on 10 October 2019 in the friendly game against Sigma Olomouc that took place at the legendary Stadion Za Lužánkami, reaching 2-0 win. On 18 October 2019, Machálek reached his first regular season win in the home match against Varnsdorf, that ended 4-1. Machálek is known for approaching a football philosophy clearly based on lively, quick and attacking play. His teams are well known for their fast, aggressive, and offensive style of play, as well as their ability to score many goals, but also for the corresponding tendency to concede them. Machálek's son Tomáš plays for SK Líšeň.