In 2011, following two stints at minor clubs Legnano and Viareggio, Scienza was named new head coach of Serie B club Brescia, guiding them until December of that year. He successively worked regularly at Serie C clubs, being in charge of teams such as Cremonese, FeralpiSalò and Alessandria. He then moved to Switzerland to guide Challenge League club FC Chiasso during the 2016–17 season.
In 2017 he took over at Serie C club Monopoli, which he coached for four seasons, apart from a short break in 2019. During his tenure at Monopoli, he achieved a third place by the end of the 2019–20 Serie C season, and consistently guiding the small Apulian club to the promotion playoffs.
On 23 June 2021, he joined Serie C club Pro Vercelli on a two-year contract.[2] He was dismissed on 5 December 2021 following a string of negative results.[3]