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My application is roughly depicted in the attached image.

enter image description here

I am sensing a Vin voltage, by dividing down with a resistive divider, then passing the signal through an opamp and an RC filter (not shown) and lastly convert with an ADC.

My concern is: what happens if the board's supply (+5V and +3.3V) is removed but Vin remains? Is that potentially harmful for the opamp / ADC?

If yes, is there a standard way to protect them against such a case?

I thought of intercepting Vin right before the divider with a MOSFET switch, but then I will probably not be able to sense very low voltages, since Vin should be larger than Vth of the MOSFET in order for the switch to be on.

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There are probably ESD clamp diodes from the input to the GND rail and power rail of each IC. So the result would have a partially or fully powered IC from the current being provided by Vin.

since Vin should be larger than Vth of the MOSFET in order for the switch to be on.

This remark doesn't make sense. You are either mistaking the gate drive voltage (the voltage between gate and source pin) for the voltage between the drain and source pins, or something else. Furthermore, for switching Vth doesn't matter becuase Vth is just when the MOSFET barely starts to turn on. When you use a MOSFET as a switch what you care about is the gate-source voltage at which the MOSFET fully turns on which would be the gate-source voltage used to obtain the rated RDson in the datasheet (or you can look at the I-V curves and calculate the RDson at any given point from the slope). You need to review how MOSFETs work in general. If you provided a schematic of what you had in mind then I wouldn't have to be so vague.

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