How to interface Raspberry Pi 3B+ with peripheral board from different power source?

As I mentioned in my question, I have an IO controller board with many digital/analog IOs, ADC IC and many relay units. It gets its power supply from a 12 V 5 A SMPS. The board has its own buck converter unit which splits 12 V to 5 V & 3.3 V respectively to provide power to each unit.

I want to control this IO board with my Raspberry Pi 3B+ GPIOs. I have a 5 V 2.5 A official power adapter to power up the RPi.

Now my question is, can I interface the RPi with the IO controller board safely? Or will there be any ground issue, though two power sources have different grounds?