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I have a manual transmission Golf 7 TSI from 2015 and when shifting in the lower gears(1->2, 2->3, 3->4) there is an audible clunk when engaging or disengaging the clutch. This however only happens when the engine is warm. For about the first 20 minutes of the drive there is no clunk. The clunk is not loud but audible when you are paying attention to it. I tried recording the sound with my phone but that didn't work.

I don't know if this is related but the clutch pedal also starts making creaking noise when the engine is hot.

I googled for a bit and most of the search result suggests the motor mounts or dog bone mount is loose. This would make sense to me if the sounds was present from the start, but on my car it only starts when the engine is hot.

What could be causing this?

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I can believe it could be an engine mount issue that manifests itself once certain parts get warm...

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Welcome! I have a 2012 Mk6 Golf TDI and managed to introduce the exact same fault that you have when I changed the timing belt. Mine was directly caused by the engine mount being mis-aligned and slightly lose. The engine mount that caused the issue on mine was the one attached to the chassis rail on the timing belt side as I'd removed it during belt replacement but I've also seen it happen before when the mount under the engine to the bulkhead has failed on my fathers old Passat.

Essentially, check all of the engine mounts as it's almost certainly where your noise is coming from.

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