The 31-year-old forward only moved to Loftus Road in the summer after bringing an end to a four-year spell at Fulham, reuniting with former manager Mark Hughes in the process
The game itself was dominated by controversy over the handshake debacle involving Anton Ferdinand and Chelsea duo John Terry and Ashley Cole, but the injury which forced the former England international off the pitch looks to be a lot more serious than first feared.
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A statement on the club's official Twitter account read: "Andy Johnson suffered an anterior cruciate ligament injury against Chelsea and is likely to be sidelined for the majority of the season."
It will come as a big blow to the club's manager Mark Hughes, who has overseen a dramatic and radical overhaul of the playing staff this summer, bringing in 11 players, including Johnson, into the squad.
The 31-year-old was hauled off at half-time during the clash with Roberto Di Matteo's side which ended in a stalemate and initial scans have confirmed the club's worst fears.
Meanwhile, on loan Manchester United defender Fabio Da Silva also faces a spell on the sidelines after picking up a hamstring strain in the same game.