I recently joined “x” company and signed a bond with a clause about paying a penalty if I leave during or after the 3-month training period. However, my offer letter (signed by HR and me, though not notarized) mentions a 6-month internship period. Since I’m currently in the internship phase, will I be penalized if I leave now?

The bond clause regarding the penalty applies after the 3-month training period. As you are currently in the 6-month internship phase, which precedes the training period, the penalty clause is not yet applicable. However, it is advisable to consult with a legal professional for specific advice based on the exact terms of your contract.