Muzzi started his career with A.S. Roma, making his debut in Serie A on 11 February 1990, in a league match against Inter ended in a 1–1 tie, and scoring his first goal the following season. With Roma, he won the Coppa Italia in 1991, also helping his side to reach an all-Italian UEFA Cup Final that season, losing out to Inter, also missing out on the 1991 Supercoppa Italiana, which was won by Sampdoria. Muzzi was loaned to Serie B club Pisa in November 1993, where he scored 8 goals in 23 games. He then returned to Roma only to be sold in November 1994 to Cagliari, where he then spent four seasons, playing a total 144 games with 31 Serie A goals and 17 in Serie B. Muzzi joined Udinese during the 1999–2000 season, spending four more seasons with the zebrette; in total, he played 103 games for the club, scoring 39 goals, winning the 2000 UEFA Intertoto Cup, which enabled the Friuli side to qualify for the UEFA Cup the following season. He then returned to Rome to join Lazio for the 2003–04 season; although he was not a regular first-team member, his performances often proved to be decisive on the pitch, as shown by his goal which enabled Lazio to avoid relegation during the 2004–05 season; during his time with the club, he won the 2003–04 Coppa Italia, also reaching the semi-finals of the 2003–04 UEFA Cup, but missed out on the 2004 Supercoppa Italiana to Milan. In September 2005, he joined Serie B side Torino, and was one of the protagonists in the granata's return to the top flight. His second season with Torino, now in Serie A, saw Muzzi scoring only 3 goals. On September 2006, at the age of 35, and after having turned down a youth coach role at Torino, he agreed a two-year contract with Serie C1's Padova. On October 2008 he announced his retirement from active football.
Coaching career
After retirement, he joined AS Roma as a youth coach in 2009, serving on a number of different positions within the club until 2015. He subsequently joined Andrea Stramaccioni's coaching staff at Panathinaikos and AC Sparta Praha. In 2019 he was named as Aurelio Andreazzoli's assistant at Empoli, following the manager also at Genoa. On 14 November 2019 he took over as head coach of Serie B club Empoli, signing a deal with the Tuscan club till the end of the 2019–20 Serie B season. He was however dismissed on 26 January 2020, following a string of disappointing results during his short tenure at the club.
