You can set up CLion to build for android by doing the following:
Install the NDK Standalone Toolchain (https://developer.android.com/ndk/guides/standalone_toolchain.html)
In CLion Preference/Settings under Build, Execution, Deployment > Toolchains, add a new toolchain for ARM, set the C compiler path to $NDK_TOOLCHAIN_PATH/arm/bin/arm-linux-androideabi-clang, set the C++ compiler path to $NDK_TOOLCHAIN_PATH/arm/bin/arm-linux-androideabi-clang++, and if you're on Windows, set the MinGW path. The toolchain tab is a fairly new feature to Clion so make sure you have a recent version of Clion.
Repeat step 2 for any other architectures you want to support
Go to Build, Execution, Deployment > CMake. Add a new profile for ARM. Set the toolchain to the ARM toolchain and set the CMake options to
-DCMAKE_CXX_FLAGS="-fPIE -fPIC -lstdc++"
-DCMAKE_AR="$NDK_TOOLCHAIN_PATH/arm/bin/arm-linux-androideabi-ar"
-DCMAKE_RANLIB="$NDK_TOOLCHAIN_PATH/arm/bin/arm-linux-androideabi-ranlib"
If you're using a Mac you will need these too in order to tell CMake to not use the isysroot option
-DCMAKE_OSX_SYSROOT="/"
-DCMAKE_OSX_DEPLOYMENT_TARGET=""
- Repeat step 4 for any other architectures you want to support
When building, set the profile to your desired architecture (instead of Debug/Release).
Ideally, you could specify the entire toolchain (ar, ranlib, etc.) through CLion instead of using CMake options, but I haven't found a way to do so yet.