Arsenal's north London derby defeat to Tottenham on Sunday saw them drop to 15th in the Premier League, their worst start to a campaign for 39 years.
But it has been a different story in Europe for Arsenal, who beat Dundalk 3-0 at the Emirates Stadium in October, having won all five Europa League group games to qualify for the last 32 of the competition.
Keegan, who will be in charge of team duties with head coach Filippo Giovagnoli banned from the touchline, said: "Yes, results aren't going well domestically for Arsenal as Mikel Arteta would have hoped.
"But at the same time has that had any negative effect on the Europa League performances? Absolutely not.
"They've blown everybody out of the water, as you would probably expect."
Keegan, a Spurs fan, confessed to catching up on the north London derby after Dundalk had beaten Shamrock Rovers 4-2 on Sunday to win the club's 12th FAI Cup.
"I had it recorded, partly through my professional role but partly because I'm a Spurs fan, and I watched it on Monday," Keegan said ahead of Thursday's Europa League clash.
"But the Europa League games are the ones we need to be looking at to how Arsenal will set up.
"They've had eight or nine bodies consistently in the same Europa League teams, quite different to what would normally start in the Premier League.
"So we won't have learned anything from the Spurs game."
There was a new face at Dundalk on Wednesday with former Northern Ireland midfielder Jim Magilton appointed as the club's new sporting director.
Giovagnoli, first-team manager Keegan and assistant coach Giuseppe Rossi have also signed new deals after securing Dundalk's return to Europe in 2021.
But Giovagnoli has been banned from the touchline against Arsenal as the Italian does not have a Pro Licence.
Dundalk were last week fined 50,000 euros for Giovagnoli 'shadow coaching' at previous Europa League games despite lacking the necessary qualifications.
Keegan said: "It would have been a pretty long and horrible week going into this game if we'd lost on Sunday.
"But when it goes in your favour, smiles are on faces and there's no thoughts of tiredness or fatigue.
"There is an element of a free shot, but we still want to give our best effort.
"We will be disappointed if we come out the other side of this group with zero points – and they may take their eye off the ball, you just don't know."