diff --git a/App/CMakeLists.txt b/App/CMakeLists.txt
index 405fd7fc9f884f59dcf47f8f9bb9727d9b8c4b16..a439e436e7b87356c01228bf22961dcff9974c12 100644
--- a/App/CMakeLists.txt
+++ b/App/CMakeLists.txt
@@ -64,8 +64,8 @@ endif()
 #   See our deployment paper (Nejati et al 2024) for explanation.
 
 if(LINUX)
-    target_link_options(${executable_name} PRIVATE
-        "-Wl,--disable-new-dtags,-rpath,\$ORIGIN/../lib")
+    set(link_flags "-Wl,-rpath,\$ORIGIN/../lib")
+    set_target_properties(${executable_name} PROPERTIES LINK_FLAGS ${link_flags})
 elseif(APPLE)
     set(MACOSX_BUNDLE_IDENTIFIER org.bornagainproject.BornAgain)
     configure_file(${CONFIGURABLES_DIR}/MacOSXBundleInfo.plist.in ${BUILD_VAR_DIR}/Info.plist @ONLY)
diff --git a/GUI/CMakeLists.txt b/GUI/CMakeLists.txt
index c2032c11f86982348ea629d40efbc19a95b6eb7d..7d2329a57f586928f79fcc07a76db83dee475dde 100644
--- a/GUI/CMakeLists.txt
+++ b/GUI/CMakeLists.txt
@@ -31,6 +31,11 @@ set(BornAgain_LIBRARIES "$CACHE{BornAgain_LIBRARIES};${lib_dir}/${libprefix}${li
 # switch OFF Qt debug output in any configuration except DEBUG
 target_compile_definitions(${lib} PUBLIC $<$<NOT:$<CONFIG:Debug>>:QT_NO_DEBUG_OUTPUT>)
 
+if(LINUX)
+    set(link_flags "-Wl,-rpath,\$ORIGIN")
+    set_target_properties(${lib} PROPERTIES LINK_FLAGS ${link_flags})
+endif(LINUX)
+
 if(BORNAGAIN_PYTHON)
     target_compile_definitions(${lib} PRIVATE -DBORNAGAIN_PYTHON)
 endif()
diff --git a/cmake/BornAgain/MakeLib.cmake b/cmake/BornAgain/MakeLib.cmake
index 22678e602dbf06db711bcddb75be68719c53c544..316e097b3937e2151e1a0b0656902bb338e98b26 100644
--- a/cmake/BornAgain/MakeLib.cmake
+++ b/cmake/BornAgain/MakeLib.cmake
@@ -68,8 +68,8 @@ function(MakeLib lib swigtmpdir source_files include_files)
     # Set runtime-location of library dependencies
     # See our deployment paper (Nejati et al 2024) for explanation.
     if(LINUX)
-        target_link_options(${lib} PRIVATE
-           "-Wl,--disable-new-dtags,-rpath,\$ORIGIN:\$ORIGIN/extra")
+        set(link_flags "-Wl,--disable-new-dtags,-rpath,\$ORIGIN:\$ORIGIN/../extra")
+        set_target_properties(${lib} PROPERTIES LINK_FLAGS ${link_flags})
     elseif(APPLE)
         target_link_options(${lib} PRIVATE
             "-Wl,-rpath,@loader_path,-rpath,@loader_path/extra")