diff --git a/CMake/UseSlicer.cmake.in b/CMake/UseSlicer.cmake.in
index ea895e9540d54d7ee42016fc3e5f746bbe8a35c4..6ef563f6570a29a517408f3e10202e92ee13e92b 100644
--- a/CMake/UseSlicer.cmake.in
+++ b/CMake/UseSlicer.cmake.in
@@ -301,9 +301,9 @@ endif()
 # Set Slicer_INSTALL_*MODULE_*_DIR variables
 #-----------------------------------------------------------------------------
 if(Slicer_BUILD_CLI_SUPPORT)
-  set(SlicerExecutionModel_DEFAULT_CLI_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/${Slicer_CLIMODULES_BIN_DIR}")
-  set(SlicerExecutionModel_DEFAULT_CLI_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/${Slicer_CLIMODULES_LIB_DIR}")
-  set(SlicerExecutionModel_DEFAULT_CLI_ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/${Slicer_CLIMODULES_LIB_DIR}")
+  set(SlicerExecutionModel_DEFAULT_CLI_RUNTIME_OUTPUT_DIRECTORY "${SlicerExecutionModel_DEFAULT_CLI_RUNTIME_OUTPUT_DIRECTORY}")
+  set(SlicerExecutionModel_DEFAULT_CLI_LIBRARY_OUTPUT_DIRECTORY "${SlicerExecutionModel_DEFAULT_CLI_LIBRARY_OUTPUT_DIRECTORY}")
+  set(SlicerExecutionModel_DEFAULT_CLI_ARCHIVE_OUTPUT_DIRECTORY "${SlicerExecutionModel_DEFAULT_CLI_ARCHIVE_OUTPUT_DIRECTORY}")
 
   set(Slicer_INSTALL_CLIMODULES_BIN_DIR "${Slicer_INSTALL_ROOT}${Slicer_BUNDLE_EXTENSIONS_LOCATION}${Slicer_CLIMODULES_BIN_DIR}")
   set(Slicer_INSTALL_CLIMODULES_LIB_DIR "${Slicer_INSTALL_ROOT}${Slicer_BUNDLE_EXTENSIONS_LOCATION}${Slicer_CLIMODULES_LIB_DIR}")
diff --git a/CMakeLists.txt b/CMakeLists.txt
index d4c77056324da65f4d3fd461dfa2c77b7e5dc6c4..806f12b111762128e08116e5810442820bf76382 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -426,6 +426,22 @@ include(SlicerApplicationOptions)
 #-----------------------------------------------------------------------------
 include(SlicerDirectories)
 
+# SlicerExecutionModel output directories
+if(Slicer_SUPERBUILD)
+  set(_sem_output_dir ${CMAKE_BINARY_DIR}/${Slicer_BINARY_INNER_SUBDIR})
+else()
+  set(_sem_output_dir ${CMAKE_BINARY_DIR})
+endif()
+if(NOT DEFINED SlicerExecutionModel_DEFAULT_CLI_RUNTIME_OUTPUT_DIRECTORY)
+  set(SlicerExecutionModel_DEFAULT_CLI_RUNTIME_OUTPUT_DIRECTORY ${_sem_output_dir}/${Slicer_CLIMODULES_BIN_DIR})
+endif()
+if(NOT DEFINED SlicerExecutionModel_DEFAULT_CLI_LIBRARY_OUTPUT_DIRECTORY)
+  set(SlicerExecutionModel_DEFAULT_CLI_LIBRARY_OUTPUT_DIRECTORY ${_sem_output_dir}/${Slicer_CLIMODULES_LIB_DIR})
+endif()
+if(NOT DEFINED SlicerExecutionModel_DEFAULT_CLI_ARCHIVE_OUTPUT_DIRECTORY)
+  set(SlicerExecutionModel_DEFAULT_CLI_ARCHIVE_OUTPUT_DIRECTORY ${_sem_output_dir}/${Slicer_CLIMODULES_LIB_DIR})
+endif()
+
 #-----------------------------------------------------------------------------
 # Slicer version number
 #-----------------------------------------------------------------------------
diff --git a/SuperBuild/External_SlicerExecutionModel.cmake b/SuperBuild/External_SlicerExecutionModel.cmake
index 04abf908d90383868bc5ca7de3e8da8d214f7a81..2b067b0188001c7c80d4cd9a2be9c89553620e3b 100644
--- a/SuperBuild/External_SlicerExecutionModel.cmake
+++ b/SuperBuild/External_SlicerExecutionModel.cmake
@@ -87,9 +87,9 @@ if(NOT DEFINED SlicerExecutionModel_DIR AND NOT Slicer_USE_SYSTEM_${proj})
       -DSlicerExecutionModel_USE_JSONCPP:BOOL=${Slicer_BUILD_PARAMETERSERIALIZER_SUPPORT}
       -DSlicerExecutionModel_LIBRARY_PROPERTIES:STRING=${Slicer_LIBRARY_PROPERTIES}
       # Output directories
-      -DSlicerExecutionModel_DEFAULT_CLI_RUNTIME_OUTPUT_DIRECTORY:PATH=${CMAKE_BINARY_DIR}/${Slicer_BINARY_INNER_SUBDIR}/${Slicer_CLIMODULES_BIN_DIR}
-      -DSlicerExecutionModel_DEFAULT_CLI_LIBRARY_OUTPUT_DIRECTORY:PATH=${CMAKE_BINARY_DIR}/${Slicer_BINARY_INNER_SUBDIR}/${Slicer_CLIMODULES_LIB_DIR}
-      -DSlicerExecutionModel_DEFAULT_CLI_ARCHIVE_OUTPUT_DIRECTORY:PATH=${CMAKE_BINARY_DIR}/${Slicer_BINARY_INNER_SUBDIR}/${Slicer_CLIMODULES_LIB_DIR}
+      -DSlicerExecutionModel_DEFAULT_CLI_RUNTIME_OUTPUT_DIRECTORY:PATH=${SlicerExecutionModel_DEFAULT_CLI_RUNTIME_OUTPUT_DIRECTORY}
+      -DSlicerExecutionModel_DEFAULT_CLI_LIBRARY_OUTPUT_DIRECTORY:PATH=${SlicerExecutionModel_DEFAULT_CLI_LIBRARY_OUTPUT_DIRECTORY}
+      -DSlicerExecutionModel_DEFAULT_CLI_ARCHIVE_OUTPUT_DIRECTORY:PATH=${SlicerExecutionModel_DEFAULT_CLI_ARCHIVE_OUTPUT_DIRECTORY}
       # Install directories
       -DSlicerExecutionModel_INSTALL_BIN_DIR:PATH=${Slicer_INSTALL_LIB_DIR}
       -DSlicerExecutionModel_INSTALL_LIB_DIR:PATH=${Slicer_INSTALL_LIB_DIR}