I have a 2009 four cylinder Venza and it started making a knocking sound when started cold. I ended up having the work done described in this Technical Service Bulletin.
The problem was that the variable valve timing assembly uses oil pressure to work properly. When you shut the engine off, the oil is supposed to stay in that assembly, but over time the seals would go bad and the oil will drain out of that assembly when the engine is not running. The next time you start the engine that assembly clatters until the oil pressure is restored.
It's hard to say whether or not that is the noise you are hearing, but it's definitely a possibility.
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