Select power supply voltage using MOSFETs

Basic P-MOS switching circuit:

The problem is that the body diode of the FET is going to conduct if an external power source is present.

You can connect two FETs in series with their body diodes opposite each other so they don't conduct when off, and get low drop-out when both are on. Here's a crappy illustration of the concept from a product:

Depending on the current needed by the motor, select a suitable N-channel MOSFET as a low side switch:

^{simulate this circuit – Schematic created using CircuitLab}

The flyback diode need not be physically at the motor coil - if the motor is not accessible, using a diode on the control board will work too - subject to somewhat greater EMI. Depending on the parasitic diode of the MOSFET for flyback voltage inhibiting is a really bad idea: Those body diodes typically have poor characteristics - High Vf and slow switching.

The MOSFET indicated here, IRLML2502, is a really inexpensive logic level MOSFET which turns on quite well at 4.5 Volts gate voltage, for motor current of ~ 3.4 Amperes. If you need greater current, alternatives like the OnSemi NVTFS5826NL can be used instead (20A @ 60V).

The low value gate resistor inhibits ringing, and limits current spikes from the GPIO pin. The pull-down ensures that the MOSFET remains off while the microcontroller is starting up or in high impedance state.