As a manager, he is mostly remembered for his successful spell with Parma during the late 1990s, with whom they won the Coppa Italia, the UEFA Cup, and the Supercoppa Italiana.

Malesani played as a midfielder throughout his career; although he was known for his good feet and tactical sense, his performances were often inconsistent and limited by his lack of pace and movement, and he spent his brief and unremarkable playing career in the lower divisions of Italian football.

Malesani left his job at Canon in 1990 order to pursue a coaching career at Serie C1 team Chievo for the Allievi youth squad.

A good Fiorentina season convinced Parma to appoint Malesani as new head coach in 1998, where he won a Coppa Italia, a UEFA Cup, an Italian Super Cup and obtained two fourth places before being sacked during the 2000–01 season.

He led his side to tenth place in the 2006–07 Serie A final table, only seven points far from relegation, being not confirmed for the following season.

[8] He was axed on 31 March 2008 following a 2–0 home defeat to Sampdoria which left Empoli down in last place in the league table.

[15] He returned to Genoa on 2 April 2012, taking over from Pasquale Marino who had previously replaced him only to be sacked a few months later.

[19] On 29 January 2014, it was announced Malesani had agreed to take over as new manager of Serie A team Sassuolo.

[21] His behaviour was criticized, but Malesani fought back during Monica Vanali's post-match interview, arguing about his colleagues using stock phrases, claiming his managerial wins and defending his conduct, which he had anticipated to the opponent's manager Gigi Delneri.

(...) Davanti a una platea gli ho detto: "Gigi, non arrabbiarti, se vinco, vado sotto la curva!

"On 16 December 2005, after a disappointing 2–2 draw against Iraklis, Malesani held a roaring press conference.

Tired of the criticisms he and Panathinaikos had received for some poor performances both from press and supporters, he defended his hard work and dedication, as well as the club's owner Giannis Vardinogiannis, in front of the journalists.

[23][24][25] Perché ci deve essere sempre un resp- un deficiente di turno qua, che paga per tutti cazzo?

12 anni, 24 allenatori: eh cazzo sarà mica sempre l’allenatore qua che deve pagare?

Con voi bisogna dire bugie e fare i ruffiani, come coi tifosi: io non lo sono cazzo!

Tutti presuntosi, ironici, ridono: “Ah eccolo, arriva il scemo di turno!” Qua si fanno le cose seriamente cazzo!

Ma dai, su, figa, su, basta!On 9 January 2010, after losing 4–3 a dramatic match at San Siro stadium against the Inter team which went on winning the treble, Malesani contested the foul leading to the free-kick Inter scored for the temporary 3-3.

[26][27] On 24 January 2010, after a 1–1 home draw against Cagliari, Siena President Massimo Mezzaroma declared his disappointment for the team performances in front of TV journalists.

Following this statement, RAI host Enrico Varriale welcomed Malesani in the post-match interview calling him "allenatore che sta un po' sulla graticola" (Italian for "manager risking his job") and anticipated that Mezzaroma would have phoned him later.

Malesani was left surprised and deeply embittered, especially because the discussion had immediately focused on off-the-pitch topics.

(...) Se uno resiste a 21 anni a questi livelli qua, non credo che sia tanto mollo.

Siete molli voi quando dite quel- queste cose qua!

Perché vi fa comodo dire 'ste cose qua, che uno è mollo!

(...) Io son fatto così, son un coraggioso, non sono un mollo.Nicknamed "Il Male" throughout his career, tactically, Malesani used an attacking style, which was inspired by the innovative style employed by Ajax during the 90s, who were coached by Dutch Manager Louis van Gaal, rather than the Italian styles popularised by Arrigo Sacchi and Nevio Scala, which were employed by many other managers in Serie A at the time, and which favoured a more balanced defensive approach.

In defence, he used an offensive sweeper in defence (Roberto Sensini) who would advance into midfield, a right-sided centre-back who would often join the attack and act as a full-back (Lilian Thuram) to assist with transitions of play, and a pure man-marking stopper as the left-sided centre-back (Fabio Cannavaro), who would mainly sit back and defend, providing balance to the team.

[1][31] Malesani also mimicked Van Gaal's use of a sweeper keeper at both Ajax and Barcelona (Gianluigi Buffon), who would not only rush out of his area to clear the ball away from danger, allowing the team to keep a high defensive line, but also build-up plays with short passes out from the back.

[32][33][34][35][36][37][38][39] The defenders would often play a high line, pressing forwards and covering the first 30 to 40 metres of the pitch with their anticipation and mobility.