diff --git a/CMakeLists.txt b/CMakeLists.txt
index f8deebfcd..a9966f5d3 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -454,15 +454,13 @@ endif()
 if (GTSAM_INSTALL_CYTHON_TOOLBOX)
   set(GTSAM_INSTALL_CYTHON_TOOLBOX 1)
   # Set up cache options
-  set(GTSAM_CYTHON_PATH "${PROJECT_BINARY_DIR}/cython" CACHE PATH "Cython source files directory path")
   # Cython install path appended with Build type (e.g. cython, cythonDebug, etc).
-  set(GTSAM_CYTHON_INSTALL_PATH "" CACHE PATH "Cython toolbox destination, blank defaults to PROJECT_BINARY_DIR/cython.build<GTSAM_BUILD_TAG>")
+  set(GTSAM_CYTHON_INSTALL_PATH "" CACHE PATH "Cython toolbox destination, blank defaults to PROJECT_BINARY_DIR/cython<GTSAM_BUILD_TAG>")
   if(NOT GTSAM_CYTHON_INSTALL_PATH)
-    set(GTSAM_CYTHON_INSTALL_PATH "${PROJECT_BINARY_DIR}/cython.build${GTSAM_BUILD_TAG}")
+    set(GTSAM_CYTHON_INSTALL_PATH "${PROJECT_BINARY_DIR}/cython${GTSAM_BUILD_TAG}" CACHE PATH "")
   endif()
-  set(GTSAM_EIGENCY_PATH ${GTSAM_CYTHON_PATH}/gtsam_eigency)
   set(GTSAM_EIGENCY_INSTALL_PATH ${GTSAM_CYTHON_INSTALL_PATH}/gtsam_eigency)
-  add_subdirectory(cython)
+  add_subdirectory(cython ${GTSAM_CYTHON_INSTALL_PATH})
 else()
   set(GTSAM_INSTALL_CYTHON_TOOLBOX 0) # This will go into config.h
 endif()
diff --git a/cmake/GtsamCythonWrap.cmake b/cmake/GtsamCythonWrap.cmake
index 3ce7f4454..797745acf 100644
--- a/cmake/GtsamCythonWrap.cmake
+++ b/cmake/GtsamCythonWrap.cmake
@@ -41,9 +41,9 @@ execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c"
 function(wrap_and_install_library_cython interface_header extra_imports install_path libs dependencies)
   # Paths for generated files
   get_filename_component(module_name "${interface_header}" NAME_WE)
-  set(generated_files_path "${PROJECT_BINARY_DIR}/cython/${module_name}")
+  set(generated_files_path "${GTSAM_CYTHON_INSTALL_PATH}/${module_name}")
   wrap_library_cython("${interface_header}" "${generated_files_path}" "${extra_imports}" "${libs}" "${dependencies}")
-  install_cython_wrapped_library("${interface_header}" "${generated_files_path}" "${install_path}")
+  # install_cython_wrapped_library("${interface_header}" "${generated_files_path}" "${install_path}")
 endfunction()
 
 function(set_up_required_cython_packages)
@@ -214,7 +214,7 @@ function(install_cython_scripts source_directory dest_directory patterns)
     list(APPEND patterns_args PATTERN "${pattern}")
   endforeach()
 
-  install(DIRECTORY "${source_directory}" DESTINATION "${dest_directory}" CONFIGURATIONS "${CMAKE_BUILD_TYPE}"
+  file(COPY "${source_directory}" DESTINATION "${dest_directory}"
             FILES_MATCHING ${patterns_args} PATTERN "${exclude_patterns}" EXCLUDE)
 endfunction()
 
diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index b0eb43c50..74725c463 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -1,21 +1,37 @@
-# Create directory where cython build files will be placed
-file(MAKE_DIRECTORY ${GTSAM_CYTHON_INSTALL_PATH})
-
 # Install cython components
 include(GtsamCythonWrap)
 
 # Create the cython toolbox for the gtsam library
 if (GTSAM_INSTALL_CYTHON_TOOLBOX)
+  # Add the new make target command
+  add_custom_target(python-install
+    COMMAND ${PYTHON_EXECUTABLE} ${GTSAM_CYTHON_INSTALL_PATH}/setup.py install
+    WORKING_DIRECTORY ${GTSAM_CYTHON_INSTALL_FULLPATH})
+
   # build and include the eigency version of eigency
   add_subdirectory(gtsam_eigency)
-  include_directories(${GTSAM_EIGENCY_PATH})
+  include_directories(${GTSAM_EIGENCY_INSTALL_PATH})
 
   # Fix for error "C1128: number of sections exceeded object file format limit"
   if(MSVC)
     add_compile_options(/bigobj)
   endif()
 
-  # wrap gtsam
+  # First set up all the package related files.
+  # This also ensures the below wrap operations work correctly.
+  set(CYTHON_INSTALL_REQUIREMENTS_FILE "${PROJECT_SOURCE_DIR}/cython/requirements.txt")
+
+  # Install the custom-generated __init__.py
+  # This makes the cython (sub-)directories into python packages, so gtsam can be found while wrapping gtsam_unstable
+  configure_file(${PROJECT_SOURCE_DIR}/cython/gtsam/__init__.py ${GTSAM_CYTHON_INSTALL_PATH}/gtsam/__init__.py COPYONLY)
+  configure_file(${PROJECT_SOURCE_DIR}/cython/gtsam_unstable/__init__.py ${GTSAM_CYTHON_INSTALL_PATH}/gtsam_unstable/__init__.py COPYONLY)
+  configure_file(${PROJECT_SOURCE_DIR}/cython/setup.py.in ${GTSAM_CYTHON_INSTALL_PATH}/setup.py)
+  install_cython_files("${PROJECT_BINARY_DIR}/cython/setup.py" "${GTSAM_CYTHON_INSTALL_PATH}")
+  # install scripts and tests
+  install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
+  install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam_unstable" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
+
+  # Wrap gtsam
   add_custom_target(gtsam_header DEPENDS "../gtsam.h")
   wrap_and_install_library_cython("../gtsam.h" # interface_header
                                   ""                  # extra imports
@@ -23,8 +39,9 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
                                   gtsam  # library to link with
                                   "wrap;cythonize_eigency;gtsam;gtsam_header"  # dependencies which need to be built before wrapping
                                   )
+  add_dependencies(python-install gtsam gtsam_header)
 
-  # wrap gtsam_unstable
+  # Wrap gtsam_unstable
   if(GTSAM_BUILD_UNSTABLE)
     add_custom_target(gtsam_unstable_header DEPENDS "../gtsam_unstable/gtsam_unstable.h")
     wrap_and_install_library_cython("../gtsam_unstable/gtsam_unstable.h" # interface_header
@@ -33,27 +50,7 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
                                     gtsam_unstable  # library to link with
                                     "gtsam_unstable;gtsam_unstable_header;cythonize_gtsam"  # dependencies to be built before wrapping
                                     )
+    add_dependencies(python-install gtsam_unstable gtsam_unstable_header)
   endif()
 
-  set(CYTHON_INSTALL_REQUIREMENTS_FILE "${PROJECT_SOURCE_DIR}/cython/requirements.txt")
-
-  # Install the custom-generated __init__.py
-  # This is to make the build/cython/gtsam folder a python package, so gtsam can be found while wrapping gtsam_unstable
-  configure_file(${PROJECT_SOURCE_DIR}/cython/gtsam/__init__.py ${PROJECT_BINARY_DIR}/cython/gtsam/__init__.py COPYONLY)
-  configure_file(${PROJECT_SOURCE_DIR}/cython/gtsam_unstable/__init__.py ${PROJECT_BINARY_DIR}/cython/gtsam_unstable/__init__.py COPYONLY)
-  configure_file(${PROJECT_SOURCE_DIR}/cython/setup.py.in ${PROJECT_BINARY_DIR}/cython/setup.py)
-  install_cython_files("${PROJECT_BINARY_DIR}/cython/setup.py" "${GTSAM_CYTHON_INSTALL_PATH}")
-  # install scripts and tests
-  install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
-  install_cython_scripts("${PROJECT_SOURCE_DIR}/cython/gtsam_unstable" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
-
-  # Install gtsam_eigency.
-  # The paths are picked up directly from the parent CMakeLists.txt.
-  install_gtsam_eigency()
-
-  # Automatically run the python installation via the setup.py
-  install(CODE
-    "execute_process(COMMAND ${PYTHON_EXECUTABLE} setup.py install
-      WORKING_DIRECTORY ${GTSAM_CYTHON_INSTALL_PATH})")
-
 endif ()
diff --git a/cython/gtsam_eigency/CMakeLists.txt b/cython/gtsam_eigency/CMakeLists.txt
index f64e45cdb..7c215e89c 100644
--- a/cython/gtsam_eigency/CMakeLists.txt
+++ b/cython/gtsam_eigency/CMakeLists.txt
@@ -4,7 +4,7 @@ include(GtsamCythonWrap)
 # so that the cython-generated header "conversions_api.h" can be found when cythonizing eigency's core
 # and eigency's cython pxd headers can be found when cythonizing gtsam
 file(COPY "." DESTINATION ".")
-set(OUTPUT_DIR "${GTSAM_CYTHON_PATH}/gtsam_eigency")
+set(OUTPUT_DIR "${GTSAM_CYTHON_INSTALL_PATH}/gtsam_eigency")
 set(EIGENCY_INCLUDE_DIR ${OUTPUT_DIR})
 
 # This is to make the build/cython/gtsam_eigency folder a python package
@@ -36,18 +36,3 @@ target_include_directories(cythonize_eigency_core PUBLIC
 add_dependencies(cythonize_eigency_core cythonize_eigency_conversions)
 add_custom_target(cythonize_eigency)
 add_dependencies(cythonize_eigency cythonize_eigency_conversions cythonize_eigency_core)
-
-# install
-function(install_gtsam_eigency)
-  install(DIRECTORY ${GTSAM_EIGENCY_PATH}
-          DESTINATION "${GTSAM_CYTHON_INSTALL_PATH}"
-          PATTERN "CMakeLists.txt" EXCLUDE
-          PATTERN "__init__.py.in" EXCLUDE
-          PATTERN "*.dir" EXCLUDE
-          PATTERN "*.make" EXCLUDE)
-  install(TARGETS cythonize_eigency_core cythonize_eigency_conversions
-          DESTINATION "${GTSAM_EIGENCY_INSTALL_PATH}")
-  install(FILES ${GTSAM_EIGENCY_PATH}/conversions_api.h DESTINATION ${GTSAM_EIGENCY_INSTALL_PATH})
-  install(FILES ${GTSAM_EIGENCY_PATH}/__init__.py DESTINATION ${GTSAM_EIGENCY_INSTALL_PATH})
-
-endfunction()