Robertson did not play a game for the Astros during the 2000 season, and instead split his season between Kissimmee, the AAA-class New Orleans Zephyrs, and Jackson; the team was renamed to the Round Rock Express that season. He spent most of his time with the Express, where he was dubbed a "superprospect" during his time there. He won 5 games and lost 10 in 25 combined pitching appearances between the three clubs that year. Robertson spent the entire 2001 season with the Express; it was the only season of his professional career where he was used solely as a relief pitcher. In 57 appearances totaling just under 75 innings, he had a 5–1 record and a 3.91 ERA. He was promoted to the Zephyrs for most of the 2002 season, and while he was told he would continue his relief work, he impressed management enough to move back into the starting rotation before the season began. In 27 starts for the Zephyrs, Robertson had a 12–8 record, a league-leading 2.55 ERA, and 114 strikeouts en route to being named the Pacific Coast League Pitcher of the Year. After the minor league season wrapped up at the end of August, the Astros purchased his contract and placed him on the major league roster.