Portenta H7 and I2C pull-up resistors

Absolutely not true.

I'll try to be kind. :slight_smile: You are really not getting the picture. Go look closely at the module schematic. R2 and R4 are connected between 5V and SCL/SDA.

The 3.3V pull ups on the module, do not appear at the board connector. Those only connect to the lines to the magnetometer IC.