Holden stepped up his return from almost two years of knee-injury hell by replacing Mark Davies to play 66 minutes of Tuesday night's 1-0 win over Peterborough - a fifth game unbeaten that moved Wanderers' to within seven points of the Championship play-off places.
"It's a hard one for Stuart because we want him to be here," Freedman told the Bolton News. "I have told him that. I want him to stay longer. I want to give him a new contract.
"But it's a difficult position for the club, where we are right now. We had to focus on where the club is at. The fans deserved better than languishing at the bottom.
"But we are moving up now so I've got to start looking at a few people for next year. Against Peterborough, he got good game time. (He showed) A brilliant attitude about fighting for the team. You want people like that here."
Holden remains pragmatic over the prospect of a new deal, with his current one set to expire in the summer.
"We've spoken briefly about it (the contract) and decided that the most important thing was me playing football," he said. "Each side is happy with the situation. It isn't the case where one side is stressed."