If I purchase Cryptomator from the official website by buying the license key and install the APK on my android device, will updates be automatic through the Play Store, or will I need to install them manually each time? Additionally, will the Play Store recognize the purchase as linked to my account, or will I always need to manually install the app via APK on new devices?
Hey and welcome to the Cryptomator Community 
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See Setup — Cryptomator Documentation regarding this question.
They are not linked, Google does not allow this so you need to firstly install the license variant via APK download or F-Droid.
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Thank you very much for your replay!
Once I installed the apk and activated the app with the license key is there any way to manage the automatic updates without using F-Droid? (only for information)
Since I read that this variant includes automatic updates, but is it the app itself?
From Setup — Cryptomator Documentation
This variant does include an automatic updater that periodically checks if there is a newer version of this app, and if so, it can be downloaded and installed directly from within the app. Using the Update Check Interval in the Cryptomator settings, you can specify how often the update check is executed.
Yes, apk-store variant gets updated via internal auto updater and e.g. fdroid variant gets updated via F-Droid.
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Thank you very much!!!