Just before the start of the 1999-2000 season in Spanish top flight, Baljić suffered rupture of both pairs of cruciate ligaments in his left knee, anterior (ACL) and posterior (PCL), after which he underwent surgery and was put off the field for prolonged rehabilitation. Subsequent loss of form caused Baljić's Real stint to turn sour pretty much immediately. Throughout the 1999–00 season, he made only 11 league appearances (8 of them as substitute), scoring just 1 goal. He never managed to secure a first team place, and the November 1999 sacking of Toshack followed by the arrival of new head coach Vicente del Bosque, marginalized Baljić even further. At the season's end, del Bosque included Baljić in the 18-man squad he took to Paris for the 2000 Champions League Final, but did not give him a single minute of action as Real beat compatriots Valencia CF.