The Three Lions head coach will be missing two players from the back four which has featured in both of their Euro Qualifiers so far, with Joe Gomez injured and Eric Dier included in Roy Hodgson’s senior squad.
And with their first game of this meet-up against Bosnia-Herzegovina coming up on Thursday afternoon, Southgate and his staff are faced with working on a new-look back four.
UEFA Euro U21 Championship
Bosnia-Herzegovina v England
12noon, Thursday 12 November
Asim Ferhatović Hase Stadion, Sarajevo
England v Switzerland
5.45pm, Monday 16 November
Amex Stadium, Brighton
Live on BT Sport
"We have two tough challenges and we’ll have to mould a new back four together," admits Southgate.
"We lost Joe Gomez to injury and with Eric going with Roy, that’s half of the back four gone with [John] Stones and [Luke] Shaw already out of the frame.
"So there won’t be too many surprises in terms of what we’ll be working on in training, as we only really have two days to prepare before the first game.
"But we’ve got some good technical players and I think the boys that have been with us for the last two months have started to understand the style of play we’re looking for and tactically how we want to play."
It’s been an encouraging start to the new campaign for Southgate’s side, who have won all three of their games so far.
Their last outing resulted in a 3-0 win over Kazakhstan in Coventry, but with the trip to Sarajevo this week before facing group leaders Switzerland in Brighton a week on Monday, the former Middlesbrough boss knows the next nine days will be a test for his group.
Watch highlights of Southgate's side in action against Kazakhstan last month
"We had some stability over the last couple of months and I was pleased with the way we played against Kazakhstan," he revealed.
"Every team wants to beat England, Bosnia have had a poor start to the group, but when we go there, to beat England will be a good opportunity for any country.
"The away games that we play are always a tough test and Switzerland will be a good game.
"They have a good youth system out there and they’ve had a good start to the group so it will be one of the key games in the group."
Tickets for the game in Brighton on Monday 16 November are on sale now, costing just £10 for adults and £5 for concessions. Click here for more details or call 0844 327 1901.