diff --git a/cmake/GtsamCythonWrap.cmake b/cmake/GtsamCythonWrap.cmake
index 4894596f6..d785b4ef8 100644
--- a/cmake/GtsamCythonWrap.cmake
+++ b/cmake/GtsamCythonWrap.cmake
@@ -145,3 +145,30 @@ function(install_cython_scripts source_directory dest_directory patterns)
 
 endfunction()
 
+# Helper function to install specific files and handle multiple build types where the scripts
+# should be installed to all build type toolboxes
+#
+# Arguments:
+#  source_files: The source files to be installed. 
+#  dest_directory: The destination directory to install to.
+function(install_cython_files source_files dest_directory)
+
+	if(GTSAM_BUILD_TYPE_POSTFIXES)
+		foreach(build_type ${CMAKE_CONFIGURATION_TYPES})
+			string(TOUPPER "${build_type}" build_type_upper)
+			if(${build_type_upper} STREQUAL "RELEASE")
+				set(build_type_tag "") # Don't create release mode tag on installed directory
+			else()
+				set(build_type_tag "${build_type}")
+			endif()
+			# Split up filename to strip trailing '/' in GTSAM_CYTHON_INSTALL_PATH if there is one
+			get_filename_component(location "${dest_directory}" PATH)
+			get_filename_component(name "${dest_directory}" NAME)
+			install(FILES "${source_files}" DESTINATION "${location}/${name}${build_type_tag}")
+		endforeach()
+	else()
+		install(FILES "${source_files}" DESTINATION "${dest_directory}")
+	endif()
+
+endfunction()
+
diff --git a/cython/CMakeLists.txt b/cython/CMakeLists.txt
index f7c5598c0..209c85f54 100644
--- a/cython/CMakeLists.txt
+++ b/cython/CMakeLists.txt
@@ -2,3 +2,14 @@
 include(GtsamCythonWrap)
 # install scripts and tests
 install_cython_scripts("${CMAKE_SOURCE_DIR}/cython/gtsam" "${GTSAM_CYTHON_INSTALL_PATH}" "*.py")
+
+
+# generate __init__.py into build folder (configured with or without gtsam_unstable import line)
+# This also makes the build/cython/gtsam folder a python package, so gtsam can be found while wrapping gtsam_unstable
+if(GTSAM_BUILD_UNSTABLE)
+   set(GTSAM_UNSTABLE_IMPORT "from gtsam_unstable import *")
+endif()
+configure_file(${CMAKE_SOURCE_DIR}/cython/gtsam/__init__.py.in ${PROJECT_BINARY_DIR}/cython/gtsam/__init__.py)
+
+# Install the custom-generated __init__.py
+install_cython_files("${PROJECT_BINARY_DIR}/cython/gtsam/__init__.py" "${GTSAM_CYTHON_INSTALL_PATH}/gtsam")
diff --git a/cython/gtsam/__init__.py b/cython/gtsam/__init__.py
deleted file mode 100644
index ee2f47b59..000000000
--- a/cython/gtsam/__init__.py
+++ /dev/null
@@ -1,2 +0,0 @@
-from gtsam import *
-from gtsam_unstable import *
diff --git a/cython/gtsam/__init__.py.in b/cython/gtsam/__init__.py.in
new file mode 100644
index 000000000..7d456023f
--- /dev/null
+++ b/cython/gtsam/__init__.py.in
@@ -0,0 +1,2 @@
+from gtsam import *
+${GTSAM_UNSTABLE_IMPORT}
diff --git a/cython/gtsam_unstable/setup.py.in b/cython/gtsam_unstable/setup.py.in
index fe6a02fbd..bd3202c8d 100644
--- a/cython/gtsam_unstable/setup.py.in
+++ b/cython/gtsam_unstable/setup.py.in
@@ -20,7 +20,8 @@ setup(
                         "${Boost_INCLUDE_DIR}"
                        ] + eigency.get_includes(include_eigen=False),
         libraries=['gtsam', 'gtsam_unstable'],
-        library_dirs=["${GTSAM_DIR}/../../"],
+        library_dirs = ["${CMAKE_BINARY_DIR}/gtsam",
+                        "${CMAKE_BINARY_DIR}/gtsam_unstable"],
         language="c++",
         extra_compile_args="${CMAKE_CXX_FLAGS}".split(),
         extra_link_args="${CMAKE_SHARED_LINKER_FLAGS}".split()))
diff --git a/gtsam_unstable/CMakeLists.txt b/gtsam_unstable/CMakeLists.txt
index eb4937cf1..7e26bca04 100644
--- a/gtsam_unstable/CMakeLists.txt
+++ b/gtsam_unstable/CMakeLists.txt
@@ -131,9 +131,6 @@ if (GTSAM_INSTALL_CYTHON_TOOLBOX)
                                     "${GTSAM_CYTHON_INSTALL_PATH}/gtsam" # install path
                                     )
     add_dependencies(gtsam_unstable_cython_wrapper gtsam_cython_wrapper)
-    # making the build/cython/gtsam folder a python package, so gtsam can be found while wrapping gtsam_unstable
-    add_custom_target(copy_gtsam_init COMMAND ${CMAKE_COMMAND} -E copy "${CMAKE_SOURCE_DIR}/cython/gtsam/__init__.py" "${CMAKE_BINARY_DIR}/cython/gtsam")
-    add_dependencies(gtsam_unstable_cython_wrapper copy_gtsam_init)
 endif ()
 
 # Build examples