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To completely disable the onboard WiFi from the firmware on the Pi3, Edit
config.txt
nano /boot/config.txt
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and add
dtoverlay=pi3-disable-wifi dtoverlay=pi3-disable-bt
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save
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If you dont’t have WiFi cards and want to prevent wpa_supplicant from starting after boot, disable service:
sudo systemctl stop wpa_supplicant.service; sudo systemctl mask wpa_supplicant.service