Stones becomes the latest in a growing list of City players sidelined by fitness issues, further complicating Pep Guardiola's preparations for a critical stretch of fixtures. The 31-year-old had made a promising return to full fitness this campaign after missing the final three months of last season, starting all three of City's Premier League matches, but has now been forced to return to Manchester after struggling with "muscle issues" during England's training camp.
England manager Thomas Tuchel confirmed the decision.
"Unfortunately, John Stones has just left. He came with minor muscle issues to camp and didn't progress the way we thought and hoped he would, so he left camp this morning. We will not take the risk - not against Andorra and unfortunately not against Serbia," said Tuchel.
City are already managing several injury concerns. Abdukodir Khusanov has also withdrawn from international duty with a calf problem, while Phil Foden missed the recent defeat to Brighton due to ongoing ankle issues. Josko Gvardiol, Mateo Kovacic, and Rayan Cherki remain unavailable, and both Rico Lewis and Nico O'Reilly have pulled out of England Under-21 commitments.
The timing couldn't be worse for Guardiola, whose side faces Manchester United in the derby on September 14, followed by a crucial Champions League opener against Napoli on September 18, and then a visit to Arsenal just three days later.
Thomas Tuchel has backed Marc Guehi's mentality after the defender's proposed move to Liverpool dramatically collapsed on deadline day, leaving Crystal Palace manager Oliver Glasner with his captain still in place ahead of their European campaign.
Aston Villa defender Ezri Konsa has admitted that the club's transfer window was severely hampered by financial restrictions, describing the impact as something that "killed" their ability to strengthen the squad.
Manchester United have been hit with another injury concern ahead of their crucial Manchester derby clash after defender Diogo Dalot withdrew from the Portugal squad due to muscle discomfort.
West Ham United right-back Aaron Wan-Bissaka is set to make his Democratic Republic of Congo debut after switching his international allegiance from England.
