In 2004/2005, Giampaolo moved to Ascoli, where he again acted as assistant coach of unknown manager Massimo Silva. This was often cited as a trick in order to allow Giampaolo to coach the team, as he was not in possess of a valid coaching licence at the time. The season ended in a good sixth place, which allowed Ascoli to play promotion playoffs, where it was defeated by Torino Calcio. However, following a serie of cancellations by the federation, Ascoli was admitted to play Serie A the next season, and both Giampaolo and Silva were confirmed to coach a team built in only two weeks, with the only goal to maintain a place in Italian top division. On February 2006, Giampaolo was disqualified for two months by the Italian Football Federation for having acted as first team head coach without a valid coaching licence. Successively, Giampaolo was admitted to join the Coverciano coaching course, and, after having saved Ascoli from relegation, he was announced as coach of Cagliari Calcio.
On September 2006, Marco Giampaolo was involved in a freak training ground accident, the 39-year-old boss was hit on the head by a wayward ball and, despite continuing with the training session, developed symptoms of concussion soon after. The coach was taken to hospital as a precautionary measure.
On December 17, 2006, after a 3-1 away defeat to Udinese in a league match, Cagliari boss Massimo Cellino announced to have sacked Giampaolo, citing coach's loss of confidence with the team. However on February 26, 2007 Cellino decided to sack Franco Colomba and reinstate Giampaolo back at the Cagliari head coach position. After having led Cagliari to avoid relegation, he was confirmed for the 2007-08, but he was sacked again on November 13 and replaced by Nedo Sonetti, leaving the rossoblu in last place with nine points (but with one match less than other teams).