On 1 July 2000, Hecking moved into management as he took over as manager at Regionalliga Nord outfit SC Verl. His debut season started competently enough, with SC Verl sat seventh at the time of the winter break. However, Hecking's proclamations that he was seeking a new position irked the club to such an extent they fired him on 31 January 2001, after just 20 games in charge.
Hecking wasn't free for long as another Regionalliga Nord side, VfB Lübeck, came calling on 27 March 2001. Again, Hecking achieved a solid job in the remaining games, leaving the club in third place, just one short of promotion. This set the basis for the following season as the team claimed the title and moved up into the 2. Bundesliga. Hecking then managed to secure VfB Lübeck a mid-table position in the 2002–03 season. The following season was not to prove so successful though, as the team slipped back down to the Regionalliga Nord, occupying the final relegation position. This proved the catalyst for VfB Lübeck to announce that they would not be extending his contract further and he left the club on 25 May 2004.
Once again, Hecking was not short of work as just a week later 2. Bundesliga side Alemannia Aachen announced that he would be taking the managerial reins at their club from July 2004, after the departure of Jörg Berger.
Hecking became manager on 7 September 2006. Hecking recovered Hannover 96 from a dismal start that left them bottom at the time of his arrival. The team also achieved a good run through to the quarter finals of the German Cup, and finished comfortably in eleventh place in the Bundesliga. On 19 August 2009 Hecking resigned voluntarily from his post after a disastrous start to the 2009–10 season.