An international tug of war appeared to be growing for McTominay after several solid displays for Jose Mourinho’s men.
The Lancastrian’s father is from Scotland and the midfielder has pledged his allegiance to Alex McLeish’s side and is in line to make his debut against Costa Rica next week.
“Discussions with our development teams have been going on with Scott for a few months,” Southgate told BBC Radio 5 Live.
“It wasn’t so much on the senior radar because I’m always conscious of what would that have meant for Harry Winks, for Lewis Cook, for Nathaniel Chalobah, who have been in our system all the way through.
“But he’s playing well and we’re always keen to speak to players who might fit into our system at some level.
“What became apparent before I had the chance to speak with him in particular, I was going to Manchester United anyway, he had made his mind up that Scotland were keen for him to play for them and he feels Scottish.
“You have to absolutely respect that decision. I think international football has to be decision of the heart so we wish him well with that.”
While McTominay has slipped through England’s fingers like Wilfried Zaha and Victor Moses, the FA is looking into Bayer Leverkusen prospect Leon Bailey.
The 20-year-old hails from Jamaica and played for their under-23s, but is still eligible for England.
Two of Bailey’s grandparents reportedly hold British passports and the FA is keeping tabs on the exciting German-based talent.
“Well, I’d have to say until a few months ago we had no indication that he was eligible for England,” Southgate said.
“That’s still a process that is ongoing and now that issue has been flagged, he’s somebody we’ll monitor more closely.”