Conroy remained one of the League's top defensive forwards in 1998–99. While he missed several games with a high ankle sprain, he scored his first career hat-trick on February 26, 1999, against the Calgary Flames and finished sixth in Selke Trophy voting that season. He faced a difficult season in 1999–2000, however, as Joel Quenneville adopted a new strategy that abandoned the concept of a checking line. Conroy struggled at both ends of the ice, and frequently found his ice time limited as a result. He finished the season with just 27 points.