diff --git a/CMakeLists.txt b/CMakeLists.txt
index 3e47224ea103..ca4cba216531 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -126,8 +126,8 @@ if(ENABLE_PROGRAMS)
 endif()
 
 ADD_CUSTOM_TARGET(apidoc
-    COMMAND doxygen doxygen/mbedtls.doxyfile
-    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+    COMMAND doxygen mbedtls.doxyfile
+    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/doxygen)
 
 if(ENABLE_TESTING)
     enable_testing()
diff --git a/Makefile b/Makefile
index d475868a710e..c18b99b2f4f3 100644
--- a/Makefile
+++ b/Makefile
@@ -103,7 +103,7 @@ lcov:
 
 apidoc:
 	mkdir -p apidoc
-	doxygen doxygen/mbedtls.doxyfile
+	cd doxygen && doxygen mbedtls.doxyfile
 
 apidoc_clean:
 	rm -rf apidoc
diff --git a/doxygen/mbedtls.doxyfile b/doxygen/mbedtls.doxyfile
index 5df1c932db01..d5b3abe750ed 100644
--- a/doxygen/mbedtls.doxyfile
+++ b/doxygen/mbedtls.doxyfile
@@ -54,7 +54,7 @@ PROJECT_LOGO           =
 # If a relative path is entered, it will be relative to the location
 # where doxygen was started. If left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = apidoc/
+OUTPUT_DIRECTORY       = ../apidoc/
 
 # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
 # 4096 sub-directories (in 2 levels) under the output directory of each output
@@ -664,7 +664,7 @@ WARN_LOGFILE           =
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 
-INPUT                  = .
+INPUT                  = ..
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
@@ -696,7 +696,7 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = configs yotta/module
+EXCLUDE                = ../configs ../yotta/module
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded