The Gunners receive £30 million a year from the airline company, but Emirates' senior vice-president, Boutros Boutros-Ghali, has revealed that the club will be paid less money if they fail to perform on the pitch.
And although Arsenal currently sit in third position in the Premier League after beating Wigan 1-0 on Saturday, the news will worry fans as the side are currently fighting with the likes of Chelsea, Everton, Tottenham and West Brom for a spot in the top four.
"There are certain clauses, from 2015, that we pay them a percentage less if they don't perform," said Boutros-Ghali.
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"The Champions League is part of the new contract. It's just to keep them on their toes. It's fair to us and fair to them."
The airline sponsor Arsenal's shirts and stadium, but are wary of receiving less exposure if Arsene Wenger's side fail to reach the Champions League and miss out on the media exposure the tournament brings.
The French manager has led the Gunners into Europe's top club competition in every single year of his reign in north London, but he is currently experiencing his worst start to a season at Arsenal with 30 points from 18 games, including four defeats.
The club are also without a trophy for seven years, but Emirates have negotiated a contract extension for another five years from the 2014-15 season, and the company believe the club are still a good investment.
Boutros-Ghali continued: "Arsenal is an incredibly strong brand, well managed, with a great coach."