diff --git a/PCLConfig.cmake.in b/PCLConfig.cmake.in
index 3df410174fc..90f4514a779 100644
--- a/PCLConfig.cmake.in
+++ b/PCLConfig.cmake.in
@@ -222,7 +222,7 @@ macro(find_flann)
   if(PCL_ALL_IN_ONE_INSTALLER)
     set(FLANN_ROOT "${PCL_ROOT}/3rdParty/Flann")
   elseif(NOT FLANN_ROOT)
-    get_filename_component(FLANN_ROOT "@FLANN_INCLUDE_DIRS@" PATH)
+    set(FLANN_ROOT "@FLANN_ROOT@")
   endif()
 
   set(FLANN_USE_STATIC @FLANN_USE_STATIC@)
diff --git a/cmake/Modules/FindFLANN.cmake b/cmake/Modules/FindFLANN.cmake
index 97decc361ac..6e558446836 100644
--- a/cmake/Modules/FindFLANN.cmake
+++ b/cmake/Modules/FindFLANN.cmake
@@ -21,6 +21,7 @@
 # ::
 #
 #   FLANN_FOUND               True in case FLANN is found, otherwise false
+#   FLANN_ROOT                Path to the root of found FLANN installation
 #
 # Example usage
 # ^^^^^^^^^^^^^
@@ -45,6 +46,10 @@ if(flann_FOUND)
   else()
     set_property(TARGET FLANN::FLANN APPEND PROPERTY INTERFACE_LINK_LIBRARIES flann::flann_cpp)
   endif()
+  # Determine FLANN installation root based on the path to the processed Config file
+  get_filename_component(_config_dir "${flann_CONFIG}" DIRECTORY)
+  get_filename_component(FLANN_ROOT "${_config_dir}/../../.." ABSOLUTE)
+  unset(_config_dir)
   return()
 endif()
 
@@ -136,4 +141,5 @@ if(FLANN_FOUND)
       endif()
     endif()
   endif()
+  get_filename_component(FLANN_ROOT "${FLANN_INCLUDE_DIR}" PATH)
 endif()
diff --git a/cmake/pcl_all_in_one_installer.cmake b/cmake/pcl_all_in_one_installer.cmake
index 718993466b9..039a21f093f 100644
--- a/cmake/pcl_all_in_one_installer.cmake
+++ b/cmake/pcl_all_in_one_installer.cmake
@@ -11,7 +11,6 @@ get_filename_component(BOOST_ROOT "${Boost_INCLUDE_DIR}" PATH)
 get_filename_component(BOOST_ROOT "${BOOST_ROOT}" PATH)
 get_filename_component(EIGEN_ROOT "${EIGEN_INCLUDE_DIRS}" PATH)
 get_filename_component(QHULL_ROOT "${QHULL_INCLUDE_DIRS}" PATH)
-get_filename_component(FLANN_ROOT "${FLANN_INCLUDE_DIRS}" PATH)
 get_filename_component(VTK_ROOT "${VTK_DIR}" PATH)
 get_filename_component(VTK_ROOT "${VTK_ROOT}" PATH)
 get_filename_component(VTK_ROOT "${VTK_ROOT}" PATH)