Media playback is not supported on this device
The 30-year-old Scot admitted there was "obviously something there" in relation to Murray's hip injury but feels his movement against Benoit Paire suggests "we shouldn't be too worried".
"There's a day off between matches and he'd a straight-sets win," said Baker.
"He has more time to let that heal."
Baker believes the truest indicator of his good friend Murray's fitness is how he moves during play, and that his ability to race to the net to return Frenchmen Paire's drop shots in their last-16 game on Monday showed he is coping with the injury.
"If it was a real concern we wouldn't see him out on the practice court in between matches so he will be ready to go for the quarter-finals," said Baker, who retired from playing in 2013.
Media playback is not supported on this device
However, while some may already be looking forward to Murray playing a semi-final against Rafael Nadal's conqueror Gilles Muller or seventh seed Marin Cilic, Baker believes Murray will have to be on his guard against the big-serving American.
"Everyone was probably looking at the draw, seeing how well Nadal had started the tournament, and thinking it could be a seriously tough match against Andy Murray in the semi-final," Baker told BBC Scotland.
"Let's not forget Sam Querrey beat (Novak) Djokovic here last year. Nothing really flusters him. He is a dangerous opponent.
"However, if you'd said Andy Murray would have Querrey in the quarters and potentially Cilic in the semis, you'd take that."
Former Wimbledon champion Goran Ivanisevic is another warning Murray, in his 10th consecutive Wimbledon quarter-final, not to under-estimate 24th seed Querrey, who beat South Africa's Kevin Anderson in five sets to reach the last eight.
"He has a big game; he has nothing to lose," said 2001 winner Ivanisevic of the American.
"Andy is the absolute favourite, he sees himself in the semi-finals already, but he has to be careful not to be too defensive because Querrey is going to go for it.
"Andy hasn't played his best tennis yet and he is in the quarter-finals, which is great. Maybe we're about to see Andy at his best."
Jamie Baker has played down concerns about Andy Murray's fitness as the world number one prepares to face America's Sam Querrey in Wednesday's Wimbledon men's singles quarter-final.