diff --git a/.circleci/config.yml b/.circleci/config.yml
index 1a00daa177..891c0684ac 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -42,7 +42,7 @@ jobs:
           command: python3 -m pytest --verbose tests/test_code_conventions.py
       - run:
           name: Check that doxygen can parse the documentation
-          command: mkdir -p build/docs && ./scripts/run_doxygen.sh doxygen docs/.Doxyfile
+          command: mkdir -p build/docs && ./scripts/run_doxygen.sh doxygen docs/.Doxyfile build/docs
 
   buildcheck:
     description: Test that we can build a single KEM/Signature pair as part of a minimal build.
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 52481ed11c..1d197e655c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -187,7 +187,7 @@ if(NOT ${OQS_BUILD_ONLY_LIB})
         set(DOXYFILE ${PROJECT_SOURCE_DIR}/docs/.Doxyfile)
         add_custom_target(
             gen_docs
-            COMMAND ${PROJECT_SOURCE_DIR}/scripts/run_doxygen.sh ${DOXYGEN_EXECUTABLE} ${DOXYFILE}
+            COMMAND ${PROJECT_SOURCE_DIR}/scripts/run_doxygen.sh ${DOXYGEN_EXECUTABLE} ${DOXYFILE} ${PROJECT_BINARY_DIR}
             WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
             COMMENT "Generate API documentation with Doxygen."
             USES_TERMINAL)
diff --git a/docs/.Doxyfile b/docs/.Doxyfile
index 421ddd3b30..20b3d9d16f 100644
--- a/docs/.Doxyfile
+++ b/docs/.Doxyfile
@@ -58,7 +58,7 @@ PROJECT_LOGO           =
 # entered, it will be relative to the location where doxygen was started. If
 # left blank the current directory will be used.
 
-OUTPUT_DIRECTORY       = build/docs
+OUTPUT_DIRECTORY       = $(DOXYGEN_DESTIONATION_DIR)
 
 # 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 format and
diff --git a/scripts/run_doxygen.sh b/scripts/run_doxygen.sh
index 7cca0bc197..3faa64cf75 100755
--- a/scripts/run_doxygen.sh
+++ b/scripts/run_doxygen.sh
@@ -2,8 +2,8 @@
 
 # SPDX-License-Identifier: MIT
 
-if [ "$#" -ne 2 ]; then
-   echo "Wrong number of arguments: Expecting path to doxygen binary and doxygen file. Exiting." 
+if [ "$#" -ne 3 ]; then
+   echo "Wrong number of arguments: Expecting path to doxygen binary, path to doxygen file, and destination directory. Exiting." 
    exit 1
 fi
 
@@ -14,7 +14,8 @@ cp CONFIGURE.md CONFIGURE.md-orig
 python3 scripts/doxyfy.py CONFIGURE.md-orig CONFIGURE.md
 
 # run doxygen:
-$1 $2
+mkdir -p "$3/docs"
+env DOXYGEN_DESTIONATION_DIR="$3/docs" "$1" "$2"
 EXITCODE=$?
 
 # undo the Github Markdown reformatting