The nRF52840 Dongle can be programmed through the built-in USB bootloader.
The Dongle can be made to enter bootloader mode in one of the two ways:
Trigger the nRF52840 USB DFU endpoint.
The firmware to support this is embedded in all nRF Connect for Desktop apps for the nRF52840 Dongle. If you add the DFU Trigger Library (USB) to your custom device firmware, you will be able to trigger the DFU from nRF Connect for Desktop without using any buttons. For documentation, see DFU Trigger Library (USB), which is part of the nRF5 SDK v15.2.0.
For Dongles with applications missing the USB DFU endpoint: Press the RESET
When the nRF52840 Dongle has entered the bootloader mode, LD2 pulses red. The Dongle is now ready for programming.
All the nRF Connect for Desktop apps require specific firmware to be present on the nRF52840 Dongle to function correctly. The apps will update the firmware if needed. If you want to upload a custom firmware to the Dongle, you can do this by using the dedicated Programmer programming app, or nrfutil.