Starting with Android 7, apps have to opt into user-installed certificates. Browsers often do (Firefox is an annoying exception, you need to turn it on in the dev settings and it doesn't work in the official release version of the browser), but apps usually don't even know that the setting exists.
Aside from that, Android has a very easy certificate pinning API where you can just assign a fingerprint to a domain name in the XML config files and it'll pin a certificate to that domain. Easy to bypass if you modify the APK file, but then you miss out on updates and other mechanisms could check if the signature has been tampered with.
With root access (shouldn't be too hard to gain on an Android device still running 7) you can add your certificate to the root certificate folder on the system partition. This will make Let's Encrypt work on all apps. It doesn't bypass certificate pinning, of course, but you don't need there for Let's Encrypt.
Aside from that, Android has a very easy certificate pinning API where you can just assign a fingerprint to a domain name in the XML config files and it'll pin a certificate to that domain. Easy to bypass if you modify the APK file, but then you miss out on updates and other mechanisms could check if the signature has been tampered with.
With root access (shouldn't be too hard to gain on an Android device still running 7) you can add your certificate to the root certificate folder on the system partition. This will make Let's Encrypt work on all apps. It doesn't bypass certificate pinning, of course, but you don't need there for Let's Encrypt.