Clark had been having a promising summer after nearly a year out with a serious ankle injury, but went down under no challenge in the match with Malahide last night and was subbed after only 10 minutes.
It is thought to be a knee injury, and Dons boss Derek McInnes fears the worst.
He said: "It doesn't look great to be honest. We will see how it is and it's too early to speculate, but he's clearly done something.
"It was serious enough for him to go down early. It's not ideal because we don't want to be picking up injuries.
"We've been trying Chris at full-back because it's an opportunity for him and because we're a bit short at full-back and this doesn't help matters.
"Our thoughts are with Chris at the moment and let's just hope it's better news than we think."
A young Aberdeen side, who featured new keeper Nicky Weaver for the first time, went an early goal down but strikes from Jamie Masson, a brace from Scott Vernon, and Nicky Low gave the Reds a 4-1 victory.