Donati started his club career at Atalanta, before moving to Milan in June 2001 along with Cristian Zenoni for 60 billion lire in a cash-plus-player deal.

Despite finding his form at Messina, Donati still found himself out of favour at Milan and was again sent on loan, this time returning to his first club Atalanta for the 2006–07 season.

[11] This result meant Celtic only needed a point away to Donati's former club Milan at the San Siro to qualify for the last 16 stage of the tournament.

[13] In the 2008–09 season, Donati made only a handful of appearances for Celtic, though he started in the home game against Kilmarnock on 12 November 2008 and won the man of the match award.

Donati played in most of the pre-season games and scored in a 5–0 win over African Champions League winners Al-Ahly in the Wembley Cup.

He started the 2009–10 campaign in fine form and scored from a spectacular volley in Celtic's 3–1 loss to Arsenal in the Champions League play-off.

[24] In January 2018, Hamilton announced that they had agreed with Donati to cancel his existing playing contract, in order for him to begin a coaching career.

[28] In 2018, Donati was unveiled as a new color commentator and pundit for DAZN, a role he left in June 2021 following his appointment as Sambenedettese's new head coach.

[29] He briefly resumed his role at DAZN between August and September 2021, leaving again after Sambenedettese was successfully readmitted into Serie D.[30][31] In June 2019, Donati joined the coaching staff at Kilmarnock under Angelo Alessio.