The airline company revealed the new contract starting from 2015 means the Gunners will receive less money if they fail to perform and don't qualify for the Champions League.
The Gunners receive 30 million pounds per year from the airline company, but Emirates' senior vice president, Boutros Boutros has revealed that the club will be paid less money if its fails to perform up to a high standard.
Arsenal currently sits in third place in the Premier League after beating Wigan 1-0 on Saturday, but the news will still be a worry as the side is currently fighting with the likes of Chelsea, Everton, Tottenhan 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," Boutros said. "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 sponsors Arsenal's shirts and stadium, but is wary of receiving less exposure if Arsene Wenger's side fails 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 is also without a trophy for seven years, but Emirates has negotiated a contract extension for another five years from the 2014-15 season, and the company believes the club is still a good investment.
"Arsenal is an incredibly strong brand, well managed, with a great coach," Boutros said.