diff --git a/doc/Makefile b/doc/Makefile
index d38b858fd72..5b9ab69cf2b 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -26,7 +26,7 @@ I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
 .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest coverage gettext
 
 doxy-code:
-	$(Q)cd .. && doxygen doc/doxygen.config
+	$(Q)doxygen zephyr.doxyfile
 
 doxy: doxy-code
 
diff --git a/doc/conf.py b/doc/conf.py
index 0e0326a2f11..eda98562da9 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -318,8 +318,8 @@ texinfo_documents = [
 #texinfo_no_detailmenu = False
 
 breathe_projects = {
-    "Zephyr": "xml",
-    "doc-examples": "xml"
+    "Zephyr": "doxygen/xml",
+    "doc-examples": "doxygen/xml"
 }
 breathe_default_project = "Zephyr"
 
diff --git a/doc/doxygen.config b/doc/zephyr.doxyfile
similarity index 94%
rename from doc/doxygen.config
rename to doc/zephyr.doxyfile
index 27e5866195a..a2579b9e131 100644
--- a/doc/doxygen.config
+++ b/doc/zephyr.doxyfile
@@ -8,7 +8,7 @@ PROJECT_NAME           = "Zephyr Project"
 PROJECT_NUMBER         =
 PROJECT_BRIEF          =
 PROJECT_LOGO           =
-OUTPUT_DIRECTORY       = doc/
+OUTPUT_DIRECTORY       = doxygen/
 CREATE_SUBDIRS         = YES
 OUTPUT_LANGUAGE        = English
 BRIEF_MEMBER_DESC      = YES
@@ -98,17 +98,19 @@ WARN_LOGFILE           =
 # Configuration options related to the input files
 #---------------------------------------------------------------------------
 INPUT                  = \
-                        include/ \
-                        include/misc/ \
-                        include/arch/x86/ \
-                        include/arch/arc/ include/arch/arc/v2 \
-                        include/arch/arm/ include/arch/arm/cortex_m \
-                        include/arch/nios2/ \
-                        lib/libc/minimal/include/ \
-                        ext/lib/crypto/tinycrypt/include/ \
-                        include/net/zoap.h \
-                        include/net/dns_client.h \
-                        tests/ztest/include/
+                        ../include/ \
+                        ../include/misc/ \
+                        ../include/arch/x86/ \
+                        ../include/arch/arc/ \
+			../include/arch/arc/v2 \
+                        ../include/arch/arm/ \
+			../include/arch/arm/cortex_m \
+                        ../include/arch/nios2/ \
+                        ../lib/libc/minimal/include/ \
+                        ../ext/lib/crypto/tinycrypt/include/ \
+                        ../include/net/zoap.h \
+                        ../include/net/dns_client.h \
+                        ../tests/ztest/include/
 INPUT_ENCODING         = UTF-8
 FILE_PATTERNS          = "*.c" "*.h" "*.S"
 RECURSIVE              = YES