Together, and with new money at their disposal, Marotta and Novellino revamped the Sampdoria squad in the 2002 transfer window, adding both experienced Serie A veterans, such as Massimo Paganin, Sergio Volpi, Fabio Bazzani, and Stefano Bettarini, along with several promising young players, such as Angelo Palombo, Maurizio Domizzi and Andrea Gasbarroni.

In 2003–04, he added to two big-name acquisitions in Cristiano Doni and Francesco Antonioli as Sampdoria finished in eighth place, just missing out on UEFA Cup qualification.

[4] In 2004,[citation needed] Marotta was appointed to serve as chief executive officer (CEO) (Italian: Amministratore delegato) of Sampdoria, in addition to his role of GM.

The 2007 transfer season also saw Marotta bring in the controversial Italian forward Antonio Cassano on a year-long loan from Real Madrid with the option to purchase the player.

After signing Cassano in full, Marotta added another highly regarded striker to Sampdoria with the purchase of Giampaolo Pazzini from Fiorentina for a fee of €9 million in January 2009.

[8][9] However, Sampdoria struggled in the 2008–09 season, finishing in 13th place in Serie A, leading Marotta to not renew the expiring contract of head coach Walter Mazzarri.

[10] Marotta also brought in several key players during the season's two transfer windows, including Daniele Mannini, Fernando Tissone, Nicola Pozzi and Marco Storari.

Behind 28 Serie A goals from the strike partnership of Antonio Cassano and Giampaolo Pazzini, and under Delniri's management, Sampdoria finished the 2009–10 season in fourth place, qualifying for the 2010–11 Champions League.

[11] In May 2010, Marotta was officially brought to Juventus by newly elected club chairman Andrea Agnelli (Agnelli role effective in October, but he start to co-opted with the board since 19 May) as GM for the Sports Area (Italian: Direttore Generale Area Sport), replacing Jean-Claude Blanc (who retained the role of chairman and CEO until October 2010).

Similar to his first transfer market upon taking over at Sampdoria, Marotta spent the first year in charge of transfer operations at Juventus making wholesale changes to the squad, acquiring 14 new players, including Miloš Krasić, Fabio Quagliarella, Alessandro Matri and Alberto Aquilani;[14]) while offloading 11 players, including selling club legend David Trezeguet and Brazilian playmaker Diego, moves which were unpopular with fans.

Henrikh Mkhitaryan, Romelu Lukaku, Achraf Hakimi, Nicolò Barella, Christian Eriksen, Andre Onana, Hakan Çalhanoğlu, Matteo Darmian, Edin Džeko, Marcus Thuram and Alexis Sánchez are some of his notable signings at the club, with many of these players contributing to Inter's recent success.