My nozzle on my Ender3 V2 is higher when it is printing than it is when I auto home it
From my experience Auto Home procedure rearly leaves Z position at 0. By default Marlin raises it to 4 mm above the bed as far as I remember. The same might be with Z offset.
Also, could you please check &quot;Initial Layer Height&quot; in Cura?
Could you check the machine's &quot;Start G-Code&quot; for presence of G91 code (this would be bed sign) and confirm it contains line G90?
There are valuable basic tips in this discussion about printing too low, so you may want to go through these hints.
Did you already manage to solve your problem?