Disclaimer: You do this at your own risk! I’ve been running my phone this way only for about an hour, this might still eat your data, make backups!
I managed to get Magisk working, here’s what you need:
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Unlocked bootloader
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adb & fastboot
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Magisk app installed
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Either the stock boot.img provided by Fairphone (check Settings → About phone → Build number for the version you need, just use the newest one if you are on a version not yet available)
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Or, if running an OS other than stock, the
boot.imgthat’s being shipped with your ROM.
Step-by-step:
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Patch the downloaded stock boot.img with Magisk
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Transfer / adb pull that patched boot.img to your PC
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Reboot to fastboot
adb reboot bootloaderand temporarily boot from the patched boot.imgfastboot boot /path/to/patched_boot.img
Do not flash that boot.img!!! -
Wait for the device to boot (took a bit longer than usual)
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Open the Magisk app (press Cancel when asked to perform Additional Setup), choose direct install and reboot
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Have fun
I tried to directly flash a patched stock boot.img, pulled boot_a and boot_b from the phone and patched those, but never could get Wi-Fi working (despite the hint in the developer docs). This way finally worked 
Performing an OTA update with Magisk installed: