And now Antonio Conte's worst nightmare has been realised after discovering the damage is worse than first feared.
It was initially thought that Morata would be able to return to action after the worldwide break, but the Spanish Football Federation have confirmed that the 24-year-old suffered a grade two hamstring tear that will likely keep him out for all of October plus two weeks into November.
The blow will keep him out for the whole of October and potentially for half of November.
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And it is not only domestically that Chelsea will feel his absence. He will also be out for the Champions League double header against Roma while being a doubt for the fixtures against West Brom and F.C. Qarabag next month.
Morata has scored seven goals in his first ten matches for the champions since his summer arrival from the Bernabeu.
The summer transfer window was one the craziest we have ever seen.
Conte admitted after the City game he took a massive risk playing Morata for the third time in seven days, but insisted he had no option but to play the frontman in such a big game. Judging by the way he has played so far, Morata could prove to be an excellent buy for Chelsea; he could go on to challenge the likes of Harry Kane and Romelu Lukaku for the Premier League Golden Boot award this season.