The Manchester City midfielder, on loan at Sheffield United, scored his first goals for the Young Lions.
Liverpool’s Harvey Elliott added a third early in the second half as England saw out their Euro 2025 qualifier on Saturday with minimum fuss, shrugging off last month’s rare defeat to Ukraine.
Lee Carsley’s side remain second, three points behind leaders Ukraine in Group F after their 4-0 win over Luxembourg on Friday.
England thumped Serbia 9-1 at the City Ground last month and were dominant from the start in Backa Topola.
It took just five minutes for the Young Lions to open the scoring when McAtee collected the ball on the edge of the area and his strike deflected off Mihajlo Ilic to loop over Veljko Ilic in goal.
Four minutes later Liam Delap came close to doubling the lead when he glanced Noni Madueke’s cross just wide.
But it was 2-0 after 19 minutes when McAtee received Hayden Hackney’s pass 20 yards out and drilled in, although Ilic should have done better.
England dominated the rest of the half without adding to their advantage but took just nine minutes of the second half to make it 3-0.
Elliott scored twice in the rout in Nottingham and got in on the act when he drilled into the bottom corner from 25 yards.
Striker Jay Stansfield, making his debut after a late call this week, hit the woodwork after a neat turn and strike with 13 minutes left and also went close late on.
Stansfield, on loan at Birmingham from Fulham, was denied a debut goal with three minutes remaining when he latched onto Madueke’s pass but saw his shot blocked.