diff --git a/doc/Doxyfile.in b/doc/Doxyfile.in
index a9f5bd055..737cff1bb 100644
--- a/doc/Doxyfile.in
+++ b/doc/Doxyfile.in
@@ -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       = @CMAKE_BINARY_DIR@/doxygen
+OUTPUT_DIRECTORY       = @PROJECT_BINARY_DIR@/doxygen
 
 # 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
@@ -144,7 +144,7 @@ FULL_PATH_NAMES        = YES
 # will be relative from the directory where doxygen is started.
 # This tag requires that the tag FULL_PATH_NAMES is set to YES.
 
-STRIP_FROM_PATH        = @PROJECT_SOURCE_DIR@ @CMAKE_BINARY_DIR@
+STRIP_FROM_PATH        = @PROJECT_SOURCE_DIR@ @PROJECT_BINARY_DIR@
 
 # The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the
 # path mentioned in the documentation of a class, which tells the reader which
@@ -153,7 +153,7 @@ STRIP_FROM_PATH        = @PROJECT_SOURCE_DIR@ @CMAKE_BINARY_DIR@
 # specify the list of include paths that are normally passed to the compiler
 # using the -I flag.
 
-STRIP_FROM_INC_PATH    = @DOXYGEN_INCLUDE_DIRS@ @CMAKE_BINARY_DIR@/include
+STRIP_FROM_INC_PATH    = @DOXYGEN_INCLUDE_DIRS@ @PROJECT_BINARY_DIR@/include
 
 # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but
 # less readable) file names. This can be useful is your file systems doesn't
@@ -731,7 +731,7 @@ WARN_FORMAT            = "$file:$line: $text"
 # messages should be written. If left blank the output is written to standard
 # error (stderr).
 
-WARN_LOGFILE           = @CMAKE_BINARY_DIR@/doxygen-warnings.log
+WARN_LOGFILE           = @PROJECT_BINARY_DIR@/doxygen-warnings.log
 
 #---------------------------------------------------------------------------
 # Configuration options related to the input files
@@ -744,7 +744,7 @@ WARN_LOGFILE           = @CMAKE_BINARY_DIR@/doxygen-warnings.log
 # Note: If this tag is empty the current directory is searched.
 
 INPUT                  = @PROJECT_SOURCE_DIR@
-INPUT                 += @CMAKE_BINARY_DIR@/include
+INPUT                 += @PROJECT_BINARY_DIR@/include
 INPUT                 += @CMAKE_CURRENT_BINARY_DIR@
 
 # This tag can be used to specify the character encoding of the source files
@@ -801,7 +801,7 @@ EXCLUDE_SYMLINKS       = NO
 # Note that the wildcards are matched against the file with absolute path, so to
 # exclude all test directories for example use the pattern */test/*
 
-EXCLUDE_PATTERNS       = */podio/* */TrickTrack/*  */tests/* */dict/* */cmake/* @CMAKE_BINARY_DIR@
+EXCLUDE_PATTERNS       = */podio/* */TrickTrack/*  */tests/* */dict/* */cmake/* @PROJECT_BINARY_DIR@
 
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the