diff --git a/doc/changelog.dox b/doc/changelog.dox
index 3bb7487cf..f21020ae0 100644
--- a/doc/changelog.dox
+++ b/doc/changelog.dox
@@ -177,6 +177,10 @@ See also:
     (the HTML markup was unchanged since 2013, heh)
 -   ES 2.0 and ES 3.0 subset of tests requiring GL context is now run on Travis
     CI using SwiftShader for better code coverage
+-   On CMake 3.13 and up, WebGL2 build on Emscripten (and the `-s USE_WEBGL2=1`
+    flag in particular) is now handled by the `FindOpenGLES3.cmake` module
+    and the new `INTERFACE_LINK_OPTIONS` property instead of `FindMagnum.cmake`. On older versions this is handled in `FindMagnum.cmake` by modifying the
+    global `CMAKE_EXE_LINKER_FLAGS` variable.
 
 @subsection changelog-latest-bugfixes Bug fixes
 
diff --git a/modules/FindMagnum.cmake b/modules/FindMagnum.cmake
index fa9a74d76..a69d24d2f 100644
--- a/modules/FindMagnum.cmake
+++ b/modules/FindMagnum.cmake
@@ -832,12 +832,6 @@ foreach(_component ${Magnum_FIND_COMPONENTS})
                     INTERFACE_LINK_LIBRARIES OpenGLES3::OpenGLES3)
             endif()
 
-            # Emscripten needs a special flag to use WebGL 2
-            if(CORRADE_TARGET_EMSCRIPTEN AND NOT MAGNUM_TARGET_GLES2)
-                # TODO: give me INTERFACE_LINK_OPTIONS or something, please
-                set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -s USE_WEBGL2=1")
-            endif()
-
         # MeshTools library
         elseif(_component STREQUAL MeshTools)
             set(_MAGNUM_${_COMPONENT}_INCLUDE_PATH_NAMES CompressIndices.h)
@@ -959,7 +953,7 @@ foreach(_component ${Magnum_FIND_COMPONENTS})
     endif()
 endforeach()
 
-# Emscripten-specific files
+# Emscripten-specific files and flags
 if(CORRADE_TARGET_EMSCRIPTEN)
     find_file(MAGNUM_EMSCRIPTENAPPLICATION_JS EmscriptenApplication.js
         PATH_SUFFIXES share/magnum)
@@ -975,6 +969,20 @@ if(CORRADE_TARGET_EMSCRIPTEN)
         MAGNUM_EMSCRIPTENAPPLICATION_JS
         MAGNUM_WINDOWLESSEMSCRIPTENAPPLICATION_JS
         MAGNUM_WEBAPPLICATION_CSS)
+
+    # If we are on CMake 3.13 and up, `-s USE_WEBGL2=1` linker option is
+    # propagated from FindOpenGLES3.cmake already. If not (and the GL library
+    # is used), we need to modify the global CMAKE_EXE_LINKER_FLAGS. Do it here
+    # instead of in FindOpenGLES3.cmake so it works also for CMake subprojects
+    # (in which case find_package(OpenGLES3) is called in (and so
+    # CMAKE_EXE_LINKER_FLAGS would be modified in) Magnum's root CMakeLists.txt
+    # and thus can't affect the variable in the outer project). CMake supports
+    # IN_LIST as an operator since 3.1 (Emscripten needs at least 3.7), but
+    # it's behind a policy, so enable that one as well.
+    cmake_policy(SET CMP0057 NEW)
+    if(CMAKE_VERSION VERSION_LESS 3.13 AND GL IN_LIST Magnum_FIND_COMPONENTS AND NOT MAGNUM_TARGET_GLES2 AND NOT CMAKE_EXE_LINKER_FLAGS MATCHES "-s USE_WEBGL2=1")
+        set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -s USE_WEBGL2=1")
+    endif()
 endif()
 
 # Complete the check with also all components
diff --git a/modules/FindOpenGLES3.cmake b/modules/FindOpenGLES3.cmake
index c9c1e02ab..413be610e 100644
--- a/modules/FindOpenGLES3.cmake
+++ b/modules/FindOpenGLES3.cmake
@@ -87,4 +87,14 @@ if(NOT TARGET OpenGLES3::OpenGLES3)
 
     set_property(TARGET OpenGLES3::OpenGLES3 PROPERTY
         INTERFACE_INCLUDE_DIRECTORIES ${OPENGLES3_INCLUDE_DIR})
+
+    # Emscripten needs a special flag to use WebGL 2. CMake 3.13 allows to set
+    # this via INTERFACE_LINK_OPTIONS, for older versions we modify the global
+    # CMAKE_EXE_LINKER_FLAGS inside FindMagnum.cmake.
+    if(CORRADE_TARGET_EMSCRIPTEN AND NOT CMAKE_VERSION VERSION_LESS 3.13)
+        # I could probably use target_link_options() here, but let's be
+        # consistent with the rest
+        set_property(TARGET OpenGLES3::OpenGLES3 APPEND PROPERTY
+            INTERFACE_LINK_OPTIONS "SHELL:-s USE_WEBGL2=1")
+    endif()
 endif()
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 5e1906212..537182a0c 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -35,9 +35,11 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC" OR CMAKE_CXX_SIMULATE_ID STREQUAL "MSVC
     string(REPLACE "/W3" "" CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
 endif()
 
-# Emscripten needs special flag to use WebGL 2
-if(CORRADE_TARGET_EMSCRIPTEN AND NOT TARGET_GLES2)
-    # TODO: give me INTERFACE_LINK_OPTIONS or something, please
+# Emscripten needs special flag to use WebGL 2. If we are on CMake 3.13 and up,
+# `-s USE_WEBGL2=1` linker option is propagated from FindOpenGLES3.cmake
+# already. If not (and the GL library is used), we need to modify the global
+# CMAKE_EXE_LINKER_FLAGS.
+if(CORRADE_TARGET_EMSCRIPTEN AND CMAKE_VERSION VERSION_LESS 3.13 AND WITH_GL AND NOT TARGET_GLES2)
     set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -s USE_WEBGL2=1")
 endif()