diff --git a/CMakeLists.txt b/CMakeLists.txt
index 2cbdbf00c..f8deebfcd 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -454,13 +454,14 @@ endif()
 if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   set(GTSAM_INSTALL_CYTHON_TOOLBOX 1)
   # Set up cache options
-  set(GTSAM_CYTHON_INSTALL_PATH "" CACHE PATH "Cython toolbox destination, blank defaults to CMAKE_INSTALL_PREFIX/cython")
-  if(NOT GTSAM_CYTHON_INSTALL_PATH)
-    set(GTSAM_CYTHON_INSTALL_PATH "${CMAKE_INSTALL_PREFIX}/cython")
-  endif()
+  set(GTSAM_CYTHON_PATH "${PROJECT_BINARY_DIR}/cython" CACHE PATH "Cython source files directory path")
   # Cython install path appended with Build type (e.g. cython, cythonDebug, etc).
-  set(GTSAM_CYTHON_INSTALL_FULLPATH "${GTSAM_CYTHON_INSTALL_PATH}${GTSAM_BUILD_TAG}")
-  set(GTSAM_EIGENCY_INSTALL_PATH ${GTSAM_CYTHON_INSTALL_FULLPATH}/gtsam_eigency)
+  set(GTSAM_CYTHON_INSTALL_PATH "" CACHE PATH "Cython toolbox destination, blank defaults to PROJECT_BINARY_DIR/cython.build<GTSAM_BUILD_TAG>")
+  if(NOT GTSAM_CYTHON_INSTALL_PATH)
+    set(GTSAM_CYTHON_INSTALL_PATH "${PROJECT_BINARY_DIR}/cython.build${GTSAM_BUILD_TAG}")
+  endif()
+  set(GTSAM_EIGENCY_PATH ${GTSAM_CYTHON_PATH}/gtsam_eigency)
+  set(GTSAM_EIGENCY_INSTALL_PATH ${GTSAM_CYTHON_INSTALL_PATH}/gtsam_eigency)
   add_subdirectory(cython)
 else()
   set(GTSAM_INSTALL_CYTHON_TOOLBOX 0) # This will go into config.h