New Bicycle - Chain making noise
Chain 'bedding in' is not a thing. Most likely the rear derailleur indexing adjustment is a little off so the chain is not running true on each sprocket. The shift and brake cable do stretch a little, requiring adjustment after a few hours riding.

If you bought the bike at a bicycle store, take it back for a tune up. In the USA this is typically done for free. If you bought it at a department or big-box store, a local bike shop will do a tune up for you.