Four problems related to manual transmission have been reported for the 2006 Toyota Matrix. The most recently reported issues are listed below.
I have a 2006 Toyota Matrix xrs 6 speed manual transmission. I purchased the car new and have serviced the car with the dealership from day one. Today I brought it in for its 45000 mile service and told them to check the clutch because we noticed it sticking/slipping in 5th gear. Turns out I need to replace the clutch at a cost of $1200 even though I have their platinum service/extended warranty plan. I haven't even worn out the brakes and I have to replace the clutch!!!! I am a 46 year old mother and have driven several cars with a manual transmission and never had to replace a clutch with such low mileage. I read on edmunds car space about this and it said to come to your website to document this.
About 10:00 pm when I was just pulling on to I-84 in downtown hartford, CT the manual transmission of my Toyota Matrix made a very loud grinding sound and I could not move. Thankfully, my momentum enabled me to get over to the side of the highway but I was still sticking out into the right lane just around a curve in the road. A state police trouper pulled behind me almost immediately and put on his lights to warn cars away. Otherwise, I am certain my car would have been rear-ended while I waited for the tow truck. The repair shop I had the car towed to said that a bearing had failed and destroyed the transmission. I had to get a completely new transmission at a cost of over $2000. This car had over 105,000 miles on it, but they were mostly highway miles and the transmission should never have failed this early.
Bearing going in 2006 Toyota Matrix 5 speed manual transmission.
Clutch had to be replaced at 35,557 miles.