diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 7311877997d9..5f0bfa0ca4d6 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -255,7 +255,8 @@ jobs:
     # Build C API documentation
     - run: curl -L https://sourceforge.net/projects/doxygen/files/rel-1.9.3/doxygen-1.9.3.linux.bin.tar.gz/download | tar xzf -
     - run: echo "`pwd`/doxygen-1.9.3/bin" >> $GITHUB_PATH
-    - run: cd crates/c-api && doxygen doxygen.conf
+    - run: cmake -S crates/c-api -B target/c-api
+    - run: cmake --build target/c-api --target doc
 
     # install mdbook, build the docs, and test the docs
     - uses: actions/cache@v4
diff --git a/crates/c-api/CMakeLists.txt b/crates/c-api/CMakeLists.txt
index ad0895c4036a..c529081e63a4 100644
--- a/crates/c-api/CMakeLists.txt
+++ b/crates/c-api/CMakeLists.txt
@@ -142,8 +142,8 @@ endif()
 
 target_include_directories(wasmtime INTERFACE ${CMAKE_CURRENT_SOURCE_DIR}/include)
 
-set(WASMTIME_GENERATED_CONF_H ${CMAKE_BINARY_DIR}/wasmtime-gen/wasmtime/conf.h)
-target_include_directories(wasmtime INTERFACE ${CMAKE_BINARY_DIR}/wasmtime-gen)
+set(WASMTIME_GENERATED_CONF_H ${CMAKE_BINARY_DIR}/include/wasmtime/conf.h)
+target_include_directories(wasmtime INTERFACE ${CMAKE_BINARY_DIR}/include)
 
 configure_file(
   ${CMAKE_CURRENT_SOURCE_DIR}/include/wasmtime/conf.h.in
@@ -157,3 +157,10 @@ install(FILES ${WASMTIME_GENERATED_CONF_H}
         DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/wasmtime)
 install(FILES ${WASMTIME_SHARED_FILES} ${WASMTIME_STATIC_FILES}
         DESTINATION ${CMAKE_INSTALL_LIBDIR})
+
+set(DOXYGEN_CONF_IN ${CMAKE_CURRENT_SOURCE_DIR}/doxygen.conf.in)
+set(DOXYGEN_CONF_OUT ${CMAKE_BINARY_DIR}/doxygen.conf)
+configure_file(${DOXYGEN_CONF_IN} ${DOXYGEN_CONF_OUT})
+add_custom_target(doc doxygen ${DOXYGEN_CONF_OUT}
+    DEPENDS ${WASMTIME_GENERATED_CONF_H} ${DOXYGEN_CONF_OUT}
+    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
diff --git a/crates/c-api/doxygen.conf b/crates/c-api/doxygen.conf.in
similarity index 99%
rename from crates/c-api/doxygen.conf
rename to crates/c-api/doxygen.conf.in
index 6c8147e11c27..b2a7c2998b75 100644
--- a/crates/c-api/doxygen.conf
+++ b/crates/c-api/doxygen.conf.in
@@ -2162,7 +2162,7 @@ SEARCH_INCLUDES        = YES
 # preprocessor.
 # This tag requires that the tag SEARCH_INCLUDES is set to YES.
 
-INCLUDE_PATH           = include
+INCLUDE_PATH           = include @CMAKE_BINARY_DIR@/include
 
 # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
 # patterns (like *.h and *.hpp) to filter out the header-files in the