diff --git a/builtins/cfitsio/CMakeLists.txt b/builtins/cfitsio/CMakeLists.txt
index f179721885b27..37a42d1c0056e 100644
--- a/builtins/cfitsio/CMakeLists.txt
+++ b/builtins/cfitsio/CMakeLists.txt
@@ -26,6 +26,13 @@ if(WIN32)
   set(patch_args --ignore-whitespace)
 endif()
 
+if(NOT EXISTS "${CFITSIO_PREFIX}/src/BUILTIN_CFITSIO/._patched")
+  set(CFITSIO_PATCH_COMMAND PATCH_COMMAND git init COMMAND git apply ${patch_args}
+                ${CMAKE_CURRENT_SOURCE_DIR}/cfitsio-no-find-zlib.diff
+                ${CMAKE_CURRENT_SOURCE_DIR}/no-fortran-wrapper.diff
+                ${CMAKE_CURRENT_SOURCE_DIR}/cfitsio-marker.diff)
+endif()
+
 ExternalProject_Add(
   BUILTIN_CFITSIO
   PREFIX ${CFITSIO_PREFIX}
@@ -43,12 +50,10 @@ ExternalProject_Add(
              -DZLIB_INCLUDE_DIR=${ZLIB_INCLUDE_DIRS}
              -DZLIB_LIBRARIES=$<TARGET_FILE:ZLIB::ZLIB>
   # Skip the find_package(ZLIB REQUIRED), because we feed CFITSIO our own ZLIB flags.
-  PATCH_COMMAND git apply ${patch_args}
-                ${CMAKE_CURRENT_SOURCE_DIR}/cfitsio-no-find-zlib.diff
-                ${CMAKE_CURRENT_SOURCE_DIR}/no-fortran-wrapper.diff
+  ${CFITSIO_PATCH_COMMAND}
   BUILD_COMMAND ${CMAKE_COMMAND} --build . ${CFITSIO_BUILD_COMMAND_FLAGS}
   INSTALL_COMMAND ${CMAKE_COMMAND} --build . ${CFITSIO_BUILD_COMMAND_FLAGS} --target install
-  LOG_DOWNLOAD 1 LOG_CONFIGURE 1 LOG_BUILD 1 LOG_INSTALL 1 LOG_OUTPUT_ON_FAILURE 1
+  LOG_PATCH 1 LOG_DOWNLOAD 1 LOG_CONFIGURE 1 LOG_BUILD 1 LOG_INSTALL 1 LOG_OUTPUT_ON_FAILURE 1
   BUILD_BYPRODUCTS ${CFITSIO_LIBRARIES}
   TIMEOUT 600
 )
diff --git a/builtins/cfitsio/cfitsio-marker.diff b/builtins/cfitsio/cfitsio-marker.diff
new file mode 100644
index 0000000000000..6be2f6ccec01a
--- /dev/null
+++ b/builtins/cfitsio/cfitsio-marker.diff
@@ -0,0 +1,4 @@
+--- /dev/null	2026-03-12 08:23:04
++++ ._patched	2026-04-28 08:20:11
+@@ -0,0 +1,1 @@
++cfitsio has been patched
diff --git a/builtins/gl2ps/CMakeLists.txt b/builtins/gl2ps/CMakeLists.txt
index 5ab968966276b..72ee0381c450d 100644
--- a/builtins/gl2ps/CMakeLists.txt
+++ b/builtins/gl2ps/CMakeLists.txt
@@ -10,7 +10,7 @@ set(ROOT_GL2PS_VERSION 1.4.2)
 set(ROOT_GL2PS_HASH "8d1c00c1018f96b4b97655482e57dcb0ce42ae2f1d349cd6d4191e7848d9ffe9")
 # Backport fix for static Win32 having being overwritten by shared lib: https://gitlab.onelab.info/gl2ps/gl2ps/-/work_items/30
 # We use all seven commits between 1.4.2 and before bump to 1.4.3
-set(ROOT_GL2PS_PATCH_FILE ${CMAKE_CURRENT_SOURCE_DIR}/v142_post_tag_fixes.patch)
+set(ROOT_GL2PS_PATCH_FILES ${CMAKE_CURRENT_SOURCE_DIR}/v142_post_tag_fixes.patch ${CMAKE_CURRENT_SOURCE_DIR}/gl2ps-marker.patch)
 
 set(ROOT_GL2PS_PREFIX ${CMAKE_BINARY_DIR}/builtins/GL2PS-prefix)
 
@@ -29,12 +29,17 @@ if(WIN32)
   set(patch_args --ignore-whitespace)
 endif()
 
+# check if the patch has already been applied
+if(NOT EXISTS "${ROOT_GL2PS_PREFIX}/src/BUILTIN_GL2PS/._patched")
+  set(GL2PS_PATCH_COMMAND PATCH_COMMAND git init COMMAND git apply ${patch_args} ${ROOT_GL2PS_PATCH_FILES})
+endif()
+
 ExternalProject_Add(
   BUILTIN_GL2PS
   PREFIX ${ROOT_GL2PS_PREFIX}
   URL ${lcgpackages}/gl2ps-${ROOT_GL2PS_VERSION}.tgz
   URL_HASH SHA256=${ROOT_GL2PS_HASH}
-  PATCH_COMMAND git apply ${patch_args} ${ROOT_GL2PS_PATCH_FILE}
+  ${GL2PS_PATCH_COMMAND}
   CMAKE_ARGS -G ${CMAKE_GENERATOR}
              -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
              -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
@@ -46,11 +51,7 @@ ExternalProject_Add(
              -DBUILD_SHARED_LIBS=OFF
   BUILD_COMMAND ${CMAKE_COMMAND} --build . ${ROOT_GL2PS_BUILD_COMMAND_FLAGS}
   INSTALL_COMMAND ${CMAKE_COMMAND} --build . ${ROOT_GL2PS_BUILD_COMMAND_FLAGS} --target install
-  LOG_DOWNLOAD 1
-  LOG_CONFIGURE 1
-  LOG_BUILD 1
-  LOG_INSTALL 1
-  LOG_OUTPUT_ON_FAILURE 1
+  LOG_PATCH 1 LOG_DOWNLOAD 1 LOG_CONFIGURE 1 LOG_BUILD 1 LOG_INSTALL 1 LOG_OUTPUT_ON_FAILURE 1
   BUILD_BYPRODUCTS ${ROOT_GL2PS_LIBRARY}
   TIMEOUT 600)
 
diff --git a/builtins/gl2ps/gl2ps-marker.patch b/builtins/gl2ps/gl2ps-marker.patch
new file mode 100644
index 0000000000000..44b7174ea80ff
--- /dev/null
+++ b/builtins/gl2ps/gl2ps-marker.patch
@@ -0,0 +1,4 @@
+--- /dev/null	2026-03-12 08:23:04
++++ ._patched	2026-04-28 08:20:11
+@@ -0,0 +1,1 @@
++gl2ps has been patched
diff --git a/builtins/libgif/CMakeLists.txt b/builtins/libgif/CMakeLists.txt
index 48a2ed37254b3..a9ad0531f7c18 100644
--- a/builtins/libgif/CMakeLists.txt
+++ b/builtins/libgif/CMakeLists.txt
@@ -28,12 +28,17 @@ if(WIN32)
   set(patch_args --ignore-whitespace)
 endif()
 
+# check if the patch has already been applied
+if(NOT EXISTS "${ROOT_LIBGIF_PREFIX}/src/BUILTIN_LIBGIF/CMakeLists.txt")
+  set(LIBGIF_PATCH_COMMAND PATCH_COMMAND git init COMMAND git apply ${patch_args} ${ROOT_LIBGIF_PATCH_FILE})
+endif()
+
 ExternalProject_Add(
     BUILTIN_LIBGIF
     PREFIX ${ROOT_LIBGIF_PREFIX}
     URL ${lcgpackages}/giflib-${ROOT_LIBGIF_VERSION}.tar.gz
     URL_HASH SHA256=${ROOT_LIBGIF_HASH}
-    PATCH_COMMAND git apply ${patch_args} ${ROOT_LIBGIF_PATCH_FILE}
+    ${LIBGIF_PATCH_COMMAND}
     CMAKE_ARGS -G ${CMAKE_GENERATOR}
     -DCMAKE_POLICY_VERSION_MINIMUM=3.5
     -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
@@ -43,7 +48,7 @@ ExternalProject_Add(
     -DCMAKE_C_VISIBILITY_PRESET=hidden
     BUILD_COMMAND ${CMAKE_COMMAND} --build . ${ROOT_LIBGIF_BUILD_COMMAND_FLAGS}
     INSTALL_COMMAND ${CMAKE_COMMAND} --build . ${ROOT_LIBGIF_BUILD_COMMAND_FLAGS} --target install
-    LOG_CONFIGURE 1 LOG_BUILD 1 LOG_INSTALL 1 LOG_OUTPUT_ON_FAILURE 1
+    LOG_PATCH 1 LOG_CONFIGURE 1 LOG_BUILD 1 LOG_INSTALL 1 LOG_OUTPUT_ON_FAILURE 1
     BUILD_BYPRODUCTS ${ROOT_LIBGIF_LIBRARY}
     TIMEOUT 600
 )