2009-10: Jonatan Nielsen played for the Linkoping U18 team and represented Sweden at the 2010 U17 World Hockey Challenge. In 34 games he scored 7 goals with 8 assists and was plus-15 with 16 penalty minutes. After finishing first in Elit South play, Linkoping was second in AllSvenskan South U18. Nielsen skated in 2 of 3 games in the playoff series with Frolunda HC and was an even plus-minus with no points or penalty minutes. He skated in all six games for Sweden at the WHC and was scoreless with 12 penalty minutes. Sweden defeated Russia in the bronze medal game.
2010-11: Nielsen split his second season with the Linkoping club between the U20 and U18 squads and represented Sweden at the U18 level – though he did not compete in the 2011 World Junior Championship. The Linkoping U20 team reached the Top 8, finishing sixth and in 29 games Nielsen scored 1 goal with 3 assists and was plus-two with 2 penalty minutes. In the three-game playoff series with MODO he was minus-two with no points or penalty minutes. Linkoping U18 finished fourth in AllSvenskan U18 after finishing first in Elit South play. Nielsen scored 3 goals with 7 assists and was plus-10 with 6 penalty minutes in 12 games. Linkoping reached the U18 quarterfinals and in five playoff games Nielsen had 1 goal with 1 assist and was minus-5 with 2 penalty minutes. In seven international matches for Sweden's U18 team he was plus-two with no points and 8 penalty minutes. Nielsen was ranked 83rd amongst European skaters in Central Scouting's final rankings prior to the 2011 NHL Draft but was not selected.
2011-12: Nielsen made his Elitserien debut, dressing in one game for Linkoping, and skated for the gold-medal winning Linkoping U20 team. Nielsen played in 38 of 48 games during the regular season as Linkoping U20 finished fourth in the South Division and 7th in the Top 10. He scored 5 goals with 4 assists; finishing plus-nine with 24 penalty minutes. Linkoping went undefeated in six playoff games, defeating HV71 in the championship game. Nielsen scored 1 goal with 3 assists and was plus-four in the playoffs. Not among the 120 European skaters in Central Scouting's final rankings, he was selected by Florida in the seventh round (194th overall) of the 2012 NHL Draft and was selected by SKA St. Petersburg in the fourth round (129th overall) of the 2012 KHL Draft.
2012-13: Nielsen saw limited ice time in six Elitserien games with Linkoping — spending most of the year playing in Allsvenskan with Sodertalje and skating for Linkoping's junior team. He had no points nor penalty minutes and averaged three minutes of ice time per game in Elitserien play. Linkoping finished fifth but Nielsen did not see any playoff action. He scored 4 goals with 4 assists in 28 games while loaned to Sodertalje and was +3 with 8 penalty minutes. Sodertalje finished second in Allsvenskan but failed to secure a promotion to the SHL; finishing last in the six-team Kval Series. Nielsen played in all 10 Kval series games and was -4 with no points and 2 penalty minutes. In 13 games with the Linkoping junior team he scored 4 goals with 4 assists and was +14 with 25 penalty minutes.
Nielsen is a tall defender with good mobility and two-way sensibilities. The son of a long-time coach in the Swedish leagues, Nielsen is well-schooled in positional defense and uses his hockey intelligence as an effective tool for disrupting opponent play in his zone. Although he has a good shot and will push the play up ice, Nielsen plays measured, low-risk game in his own zone.
Nielsen will start the season on loan to Troja-Ljunby in the Swedish second-tier league. Extended play in the Swedish leagues will be a tremendous boost to his development, and should prepare him for an eventual debut in North America.