The campaign started well with a Supercup victory over Bayern but they suffered their first major setback when influential playmaker Kevin De Bruyne joined Manchester City for a reported 75 million euros (£60.7 million) in late August.
Wolfsburg then had to deal with the potential fallout from car maker and owner Volkswagen's emissions scandal, fearing it could hurt their finances.
Things got even worse during the middle of the campaign when Bas Dost, the club's top scorer last season, suffered a broken foot during the winter break.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
Wolfsburg's attacking options were depleted further when Nicklas Bendnter was barred from training after the Danish striker, who has disappointed since arriving from Arsenal in 2014, was accused of lacking commitment by club bosses.
A recent slump in form has seen Wolfsburg score just once in their last three league games and slip down to eighth in the Bundesliga, leaving coach Dieter Hecking pondering the prospect of no European football of any kind next season.
However, when Wolfsburg handed 10-time champions Real Madrid a first defeat in the tournament this season, their fortunes were instantly revived by a stunning quarter-final debut in Europe's elite competition.
"We did everything we had set out to do and that was to play with courage, control the ball and use our speed," sports director Klaus Allofs told reporters.
"There were a lot of people who expected us to lose heavily against Real. But it did not happen. We will now try to get something out of this starting position," he said of next Tuesday's return leg in Madrid.
While the two-goal advantage may still not guarantee a spot in the last four, Wolfsburg have every right to be brimming with confidence after they neutralised the threat posed by Real's potent attack on the biggest European night in club history.
"We know what to expect there," Hecking added. "But we are in a position to score a goal and eliminate Real from the competition."
The story was refiled to fix a typo in the penultimate paragraph
(Editing by John O'Brien)
