In those two seasons in the Saporta Cup, he helped develop two national team players to the international scene, Sani Bečirovič and Goran Jurak.

However, in domestic competitions, Pipan reached two finals but failed to win any trophies, as some key players, including Boštjan Nachbar and Mileta Lisica, were struggling with injuries.

In 2000, he took over Krka and led them in the Suproleague, EuroLeague, domestic competitions and in the first edition of the Adriatic League, until he was replaced with Neven Spahija in December 2001.

After a brief episode with Zagorje, Pipan returned to Pivovarna Laško in the 2003–04 season, where he won the Slovenian Cup and lost in the league final to Olimpija.

After two months in charge, he won the Polish Cup by beating the EuroLeague team Prokom Trefl Sopot in the final.