In 1967 Künnecke started his coaching career with SC Tuttlingen, a small amateur club in the south of the Black Forest.
Afterwards, Künnecke moved to second division Racing Mechelen and won the title and were promoted in the 1974–75 season, but were relegated a year later.
Basel's youngsters played well during this season, Fredy Grossenbacher, Martin Jeitziner, Peter Nadig, Thomas Hauser and Beat Sutter advanced well under Künnecke.
Künnecke reacted immediately and this was the last game that the three veterans Arthur von Wartburg, Jörg Stohler and Jean-Pierre Maradan played in the team.
In the meantime, Basel had suffered relegation, Röthlisberger had sacked Urs Siegenthaler and then he re-installed Künnecke as head coach.
Künnecke settled in Switzerland and stayed with the club nearly three years, until in March 1992 chairman Röthlisberger released him from his position, due to a run of poor results.