diff --git a/CMakeLists.txt b/CMakeLists.txt
index eaa0fea27ad7..fdcac39b2a9a 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -14,6 +14,16 @@ set(CONF_FILE_BUILD_TYPE ${CONF_FILE_BUILD_TYPE} CACHE INTERNAL "The build type"
 # Customize the Zephyr kernel version.h using nRF Connect SDK ncs_version.h.
 set(KERNEL_VERSION_CUSTOMIZATION \#include;<ncs_version.h> PARENT_SCOPE)
 
+foreach(runner_ext BIN HEX ELF)
+  zephyr_get(NCS_RUNNER_${runner_ext} SYSBUILD)
+  if(DEFINED NCS_RUNNER_${runner_ext})
+    string(TOLOWER "${runner_ext}" type)
+    set_target_properties(runners_yaml_props_target PROPERTIES
+                          "${type}_file" "${NCS_RUNNER_${runner_ext}}"
+    )
+  endif()
+endforeach()
+
 include(cmake/extensions.cmake)
 include(cmake/version.cmake)
 include(cmake/multi_image.cmake)
diff --git a/cmake/sysbuild/partition_manager.cmake b/cmake/sysbuild/partition_manager.cmake
index 9699dbac0531..07cee5cfb966 100644
--- a/cmake/sysbuild/partition_manager.cmake
+++ b/cmake/sysbuild/partition_manager.cmake
@@ -299,21 +299,34 @@ function(update_runner)
 
   set(runners_content_update)
   file(STRINGS ${runners_file} runners_content)
-  foreach(line ${runners_content})
-    if(DEFINED RUNNER_ELF AND ${line} MATCHES "^.*elf_file: .*$")
+  foreach(line IN LISTS runners_content)
+    if(DEFINED RUNNER_ELF AND "${line}" MATCHES "^.*elf_file: .*$")
       string(REGEX REPLACE "(.*elf_file:) .*" "\\1 ${RUNNER_ELF}" line ${line})
+      set(${RUNNER_IMAGE}_NCS_RUNNER_ELF "${RUNNER_ELF}" CACHE INTERNAL
+          "nRF Connect SDK partition managere controlled elf file"
+      )
     endif()
 
-    if(DEFINED RUNNER_HEX AND ${line} MATCHES "^.*hex_file: .*$")
+    if(DEFINED RUNNER_HEX AND "${line}" MATCHES "^.*hex_file: .*$")
       string(REGEX REPLACE "(.*hex_file:) .*" "\\1 ${RUNNER_HEX}" line ${line})
+      set(${RUNNER_IMAGE}_NCS_RUNNER_HEX "${RUNNER_HEX}" CACHE INTERNAL
+          "nRF Connect SDK partition managere controlled hex file"
+      )
     endif()
 
-    if(DEFINED RUNNER_BIN AND ${line} MATCHES "^.*bin_file: .*$")
+    if(DEFINED RUNNER_BIN AND "${line}" MATCHES "^.*bin_file: .*$")
       string(REGEX REPLACE "(.*bin_file:) .*" "\\1 ${RUNNER_BIN}" line ${line})
+      set(${RUNNER_IMAGE}_NCS_RUNNER_BIN "${RUNNER_BIN}" CACHE INTERNAL
+          "nRF Connect SDK partition managere controlled bin file"
+      )
     endif()
     list(APPEND runners_content_update "${line}\n")
   endforeach()
   file(WRITE ${runners_file} ${runners_content_update})
+
+  # NCS has updated the cache with an NCS_RUNNER file, thus re-create the sysbuild cache.
+  # No need for CMAKE_RERUN in this case, as runners.yaml has been updated above.
+  sysbuild_cache(CREATE APPLICATION ${RUNNER_IMAGE})
 endfunction()