A three-time Úrvalsdeild Domestic Player of the Year, he won the Icelandic championship five times and the FIBA Europe League once.

His stay was cut short when allegations rose that he and teammate Jack Michael Martínez had been illegally recruited by coach Wayne Merino.

[4][5] Following his high school career, Jón returned to KR in time for the 2000 Úrvalsdeild karla playoffs and helped the club win the national championship.

[11] On 28 April 2018 Jón Arnór won his fourth Icelandic championship after KR defeated Tindastóll in the Úrvalsdeild finals.

[17] In January 2022, Jón Arnór returned to the floor with KR-b in the Icelandic third-tier 2. deild karla.