Stones endured an indifferent first campaign with City, but the defender has been excellent since the start of the current season with six clean sheets being recorded in 11 Premier League games.
Guardiola has suggested that players no longer get a period to ease into life at a new club, but the Spaniard has acknowledged that it was difficult for Stones to make the transition after leaving the Toffees.
The 46-year-old is quoted by Sky Sports News as saying: "We cannot forget that last season was the first time he was able to play three games a week, because Everton play once a week. Here, he immediately plays Champions League, and you need a process to settle that.
"To play in the Champions League, you have to live the experience. To be better playing in the Champions League, you have to play a lot of games. They have a lot of skills and talent when you buy them, but you have to live situations to realise, 'ok, I can handle this'.
"For that, you need time. I agree in football today you don't have time."
Stones has scored five times in 58 appearances for City in all competitions since August 2016.