He stayed with Zagreb in the newly established Croatian football league and helped achieve the best results in the club's history.
After a short episode in Austria, he returned to Zagreb and in 1996–97 season made it to the Cup finals in which they lost undeserved with the referee help to Dinamo 1–2 at Maksimir.
For Zagreb he played a total of 244 games in eleven seasons on three occasions and as a defensive player scored five goals.
Biškup made his debut for Croatia in a June 1991 friendly match away against Slovenia, coming on as an 80th-minute substitute for Aljoša Asanović, and earned a total of 5 caps scoring no goals.
In that season NK Lučko made a league record away win against the club which he also managed before, HNK Suhopolje, 7–0.
In season 2017/2018 after Besnik Prenga was sacked, it was announced that Drazen Biskup will replace him and join his former club one more time.