The midfielder has been out-of-favour at Portman Road and Tractor Boys chief Roy Keane accepted Colchester's loan bid.
But the Republic of Ireland Under-21 captain turned down the move and pledged to fight for a first-team berth at the Championship basement club.
Boothroyd told the Evening Star: "It's fair to say I did enquire about Owen and Ipswich were prepared to let him go out on loan.
"He elected to stay and fight for his place and that's fine. I've not got an issue with that. Players have to make decisions and if I had a pound for every player that didn't sign for me at Watford I'd have probably bought this club rather than be manager of it!"
He added: "That ship (regarding Garvan) has now sailed, I'm not bothered about it and we'll move on."