After being sidelined through injury for the first half of the 2000–01 season with Fiorentina, Morfeo briefly returned to Atalanta on loan the following January; during this time, however, he struggled with injuries and due to his character, and ultimately failed to consistently replicate the quality performances he had managed during his first spell with Atalanta, despite some promising performances, and a respectable tally of five goals in 17 appearances. After Fiorentina's financial difficulties had forced the club to sell several key players, Morfeo returned to the side for the 2001–02 season, and was now expected to be a central figure for the club; however, Fiorentina endured a difficult season, which ultimately ended with relegation to Serie B and bankruptcy, while Morfeo was limited to just two goals in 18 appearances, once again due to injury troubles.