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."
Manchester City secured a second successive Premier League victory at home against Sunderland, Chelsea were held scoreless away to Bournemouth while Tottenham managed to beat Brentford.
Manchester City manager Pep Guardiola insists his side are moving in the right direction as they continue to evolve following an off-season of significant rebuilding.
Pep Guardiola admitted he "did not have an answer" for Manchester City's collapse in a chaotic 5-4 victory at Fulham on Tuesday night.
Manchester City were made to work hard before eventually beating Leeds United 3-2 in their Premier Leaue clash at the Etihad Stadium on Saturday.
