Lyon felt that they had a deal done to sign him until Manchester United hijacked the deal by agreeing on a fee with Feyenoord on Monday night.
Feyenoord sporting director Frank Arnesen confirmed the agreement on Tuesday and Manchester United have agreed to pay a fee of €15m and another €2m in add-ons.
Malacia has already informed Lyon that he will not be joining and Manchester United have been in talks with his representatives over personal terms.
And according to Dutch magazine Voetbal International, an agreement is almost in place between Manchester United and Malacia to move to Old Trafford.
Personal terms are being worked out and only a few final details are left before the deal is finalised.
The Dutch left-back has chosen to agree to a move to Manchester United over joining Lyon.
Erik ten Hag has wanted Malacia since he was at Ajax and pushed Manchester United to sign him this summer.
He is likely being signed as the understudy to Luke Shaw who could remain the first-choice left-back next season.
