In 2006, Benali joined Japanese club Vissel Kobe as an assistant to Stuart Baxter. He served as a technical assistant at Racing de Santander from 2007 to 2008. Later he joined the coaching team of Baxter with the Finland national team until 2009. From 2009 to 2011, he served as the CEO of Maghreb de Fès in Morocco and director of football at Al Dhafra in the UAE. He oversaw the Spanish Sports Academy in the UAE from 2010 to 2014. Later, he headed the La Manga Club high performance soccer centre for two years.[3]
In 2016, Benali returned to Morocco as the sporting director of Botola club Moghreb Tétouan. Between 2017 and 2019, he served as the manager of Chabab Rif Al Hoceima in two stints.[4] Later, until 2020, he had a short stint as the sporting director of Moghreb Tétouan again.
In January 2020, Benali was appointed as the manager of Botola club Ittihad Tanger[5] and remained in charge until the end of the 2019–20 season.[6]
On 18 March 2021, Benali was appointed as the manager of Botola club RS Berkane. He was sacked on 23 June after a loss against Wydad AC[7]
On 18 April 2022, Benali was shortly re-appointed as the manager of Ittihad Tanger.[8]
NorthEast United
On 22 May 2023, Benali was appointed as the head coach of Indian Super League club NorthEast United on a one-year deal with an option to extend for another year.[9] He led NorthEast to the semifinals of the 2023 Durand Cup but lost to East Bengal on penalties.[10] On 3 January 2024, NorthEast United extended his contract until the end of the 2024–25 season with an option to extend for a further season.[11]