The Premier League champions opened the City Football Academy earlier this week amid much publicity, with the complex designed to improve the club's reputation in producing homegrown players.
With captain Vincent Kompany suggesting it would help build a "legacy and culture" at the club, Scholes acknowledged the impact it will likely have.
Scholes - part of the famous 'Class of '92' at Old Trafford - said that as a United fan he is "worried" by City's developments.
The former midfielder also suggested it could prove a game-changer in terms of football in the city.
"When I was a kid, it was the case among the lads I played football with that if Manchester United wanted to sign you then joining Manchester City was not even a consideration," he wrote in his column for The Independent.
"United did not have to persuade or offer inducements. We would have walked there ourselves.
"Thirty years on, and the picture in Manchester is very different and, as a United fan, it worries me.
"Trying to look at it from a neutral perspective I have to say that what City have achieved is impressive and their impact on the youth scene in Manchester began long before the opening of their City Football Academy this week
"Things change and you can take nothing for granted.
"In the modern era, United, with their history of being the greatest talent producer, have to watch that they do not become second choice in their own city."
