Arsenal made a loss of £3.4m after tax in the first half of the fiscal year due to higher than reported transfer costs.
Although the club only signed veteran goalkeeper Petr Cech for just over £10m in the summer, clauses triggered in previous deals took Arsenal's total transfer outlay to £39.4m.
That, combined with just £0.3m raised in player sales compared to £26.7m a year earlier, contributed to the disappointing result.
Transfers aside, the club's cash generating abilities did not desert the North Londoners: turnover increased by £10m to £158m in the period ended 30 November 2015 thanks to its strengthening commercial muscle and a growth in Champions League TV money.
Arsenal's commercial revenue is traditionally smaller than what it makes from ticket sales at the 60,000 capacity Emirates Stadium, yet it increased by nearly £3m to £40.9m in the period while matchday revenues fell by almost £2m to £41m.
With a cash balance of £159.4m, Arsenal's underlying financial position remains strong.
"This has been an unpredictable Premier League season thus far," said the club's chairman Sir Chips Keswick.
"What is important is that we are in contention and I am sure we have the resources and ability within the squad to sustain a strong challenge.
"The end of season run-in is going to be an exciting one and I am confident we will be very much at the centre of the action.
“We continue to see robust growth around our commercial revenues and build our support globally through our marketing and media channels. The result for the period has been impacted by a reduction in transfer profits but this reflects the overall stability we have within the squad which, in my view, is a positive factor for the club.”