diff --git a/docs/Doxyfile b/docs/Doxyfile
index 62aa1d7..e0d232a 100644
--- a/docs/Doxyfile
+++ b/docs/Doxyfile
@@ -865,7 +865,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ./README.md ./wolftpm/doxygen.h ./wolftpm/tpm2.h ./wolftpm/tpm2_wrap.h
+INPUT                  = ./docs/README.md ./wolftpm/doxygen.h ./wolftpm/tpm2.h ./wolftpm/tpm2_wrap.h
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -1063,7 +1063,7 @@ FILTER_SOURCE_PATTERNS =
 # (index.html). This can be useful if you have a project on for instance GitHub
 # and want to reuse the introduction page also for the doxygen output.
 
-USE_MDFILE_AS_MAINPAGE = README.md
+USE_MDFILE_AS_MAINPAGE = docs/README.md
 
 #---------------------------------------------------------------------------
 # Configuration options related to source browsing
diff --git a/docs/generate_documentation.sh b/docs/generate_documentation.sh
index 8f5675d..3addbef 100755
--- a/docs/generate_documentation.sh
+++ b/docs/generate_documentation.sh
@@ -1,14 +1,14 @@
 #!/bin/bash
 
 CURRDIR=${PWD##*/}
-if [ "$CURRDIR" != "docs" ]; then
-    echo "Please run from the ./docs directory"
+if [ "$CURRDIR" = "docs" ]; then
+    echo "Please run from the wolfTPM root directory"
     exit 1
 fi
 
 # Run from ./docs
 echo "Generating html..."
-doxygen Doxyfile
+doxygen ./docs/Doxyfile
 echo "Finished generating html..."
 
 echo "To view the html files use a browser to open the index.html file located at docs/html/index.html"