@hjk321 said in Xbox One Controller won't connect the "official" way but WILL connect via bluetoothctl.:

So at first glance it might seem like a xpadneo issue, but it's actually not

It could be, if your controller has the latest firmware, but xpadneo's version is less than v0.9.2.
Update your RetroPie-Setup script, and then re-install xpadneo. Try pairing the controller again - either through the RetroPie menus or via bluetoothctl.

@fahadshery
Also make sure that it's not a USB3 problem.
RF interference from the USB3 ports on a Raspberry Pi 4 can knock out the 2.4Ghz Wifi band and the Bluetooth randomly. It can work fine one day and not the next.
I would remove any USB3 cables (by putting them in the USB2 ports) and reboot.
I was even forced to use a small USB2 extension cord on my NESPi case just to keep the USB3 SATA adapter stable. (it makes the device work at USB2 speeds)

Better explained here:

It's not Pi specific, but the bad shielding on certain USB3 devices on a Pi can make it worse.

Try installing the xpadneo driver from RetroPie-Setup (see here on how to install things in RetroPie) and try re-pairing the controller again via Bluetooth.

Got it fixed. Had to use a keyboard to accept the "Yes or No" prompt when on other versions I have been able to put the PS4 controller into pairing mode and then reconnected it, select it, and then hit "Yes or No". Working now, Thank you!