The Spain international suffered anterior cruciate ligament damage last season and was sidelined for close to six months before returning at the Club World Cup.
The 29-year-old has suffered a series of minor setbacks while he played minutes this season and missed last week's 5-1 win over Burnley due to pain in the knee.
Rodri then played 60 minutes in the 2-2 draw against Monaco in the Champions League in midweek and Guardiola has urged everyone to be patient with the 2024 Ballon d'Or winner.
Speaking to reporters ahead of the clash against Everton on Sunday, the Man City mentor said: "Rodri is an outstanding player, everyone knows it.
"Maybe he struggled to understand it's not about six months or 12, the World Cup will be the best Rodri, and next season will be the best Rodri.
"This year is how to handle it. One year he has been out. The body changes, the rhythm changes, it's a question of time, if he's healthy he will be back."
City suffered their first trophyless campaign for eight years last season, and Guardiola is encouraged by the progress the team has made after refreshing his squad with new signings.
Guardiola's charges are currently five points behind league leaders Liverpool after six matches heading into this weekend's fixtures.
He added: "The happiest feeling is how we have improved. I love that feeling. And the feeling that I think we can do better.
"That is the feeling that I like as a manager. The feeling we are creating again – the tempo, the pace.
"Everything is a little bit more fluid and consistent. But we can do better, and I love that."
Nicolas Jackson scored twice as Aston Villa beat Manchester City 2-1 to end the visitors' perfect start to the Premier League season. The victory also extended Villa's unbeaten run in all competitions to seven matches.
Erling Haaland will be available for Manchester City's Premier League trip to Aston Villa on Saturday after recovering from the knock that ruled him out of their 5-1 Champions League victory over AEK Athens.
Enzo Maresca has made it his mission to help Phil Foden rediscover his best form and re-establish himself as one of England's leading players after the Manchester City midfielder ended his goal drought in spectacular fashion.
Manchester City head coach Enzo Maresca heaped praise on Phil Foden after the England international scored a hat-trick in their Champions League 5-1 victory against AEK Athens.
