Bony was unable to travel with the first-team squad for their pre-season tour of Australia and Vietnam.
The Ivory Coast international has now recovered but is staying in Manchester to continue working on his fitness at the City Football Academy.
Bony told City TV: “I was ill, now it is okay. I feel stronger than last week, so I am happy about that.
“At the beginning it was hard. There were a lot of discussions with the coach and doctor but they said it was better for me to stay here than almost 24 hours flying.
“I was a little bit disappointed but I did not choose to be ill. I have had to deal with that. Now I am okay, I am very happy and training. I think everything is clear so I am just waiting to do my best for the season.”
Bony signed for City from Swansea in a £28m deal in January but has struggled to make an impact. He missed a month due to the Africa Cup of Nations and the rest of the campaign was blighted by ankle and knee problems.
But he is now determined to make up for lost time.
He said: “Before the end of the season I came from Africa to join another team. You need to change a lot of things, and you need to train and be ready for the games, so it is not easy.
“I can say there were good moments and bad moments – but it is more important to think about what is coming now. It is about getting fit and trying to do my best for the new season.”