We moved in to this house about two months ago. We did some home improvements. We changed the hallway floors to natural stone. Completely remodeled all three bathrooms. Added and changed all the recess lighting. And painted the house inside and out.

Now We here a lot of cracking sounds. Loud enough to wake us up at nights.
Is this something we should worry about or would it go away with time.
The house was originally Built in 1956.

Unless its crackling fire so far so good Now what does the natural stones weight lay on for a sub floor wood or concrete. If its on wood could be a problem. Also quick hot and cold can cause cracking ling sounds in the floors. See if there is a correlation of quick Temp changes to sound.
Signed 21 boat

From what you say this is your first cold season in the house and these sounds might be normal, for this house. More likely than not the added weight of the stone and remodeling needs time for resettling. The original house probably stopped settling back in 1957