diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 0b9b24d98..e6dec4daf 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -37,8 +37,6 @@ jobs:
     steps:
       - name: Checkout k-NN
         uses: actions/checkout@v1
-        with:
-          submodules: true
 
       # Setup git user so that patches for native libraries can be applied and committed
       - name: Setup git user
diff --git a/.github/workflows/test_security.yml b/.github/workflows/test_security.yml
index e0f2dbf45..77b726a69 100644
--- a/.github/workflows/test_security.yml
+++ b/.github/workflows/test_security.yml
@@ -37,8 +37,6 @@ jobs:
     steps:
       - name: Checkout k-NN
         uses: actions/checkout@v1
-        with:
-          submodules: true
       # Setup git user so that patches for native libraries can be applied and committed
       - name: Setup git user
         run: |
diff --git a/CHANGELOG.md b/CHANGELOG.md
index bf09e3f49..e1f111660 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -27,6 +27,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 * Release memory properly for an array type [#1820](https://github.com/opensearch-project/k-NN/pull/1820)
 * FIX Same Suffix Cause Recall Drop to zero [#1802](https://github.com/opensearch-project/k-NN/pull/1802)
 ### Infrastructure
+* Apply custom patch only once by comparing the last patch id  [#1833](https://github.com/opensearch-project/k-NN/pull/1833)
 ### Documentation
 ### Maintenance
 ### Refactoring
diff --git a/jni/cmake/init-faiss.cmake b/jni/cmake/init-faiss.cmake
index befed4703..c2ec24a3b 100644
--- a/jni/cmake/init-faiss.cmake
+++ b/jni/cmake/init-faiss.cmake
@@ -12,20 +12,44 @@ if (NOT EXISTS ${FAISS_REPO_DIR})
     execute_process(COMMAND git submodule update --init -- external/faiss WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
 endif ()
 
-# Check if patch exist, this is to skip git apply during CI build. See CI.yml with ubuntu.
-find_path(PATCH_FILE NAMES 0001-Custom-patch-to-support-multi-vector.patch 0002-Enable-precomp-table-to-be-shared-ivfpq.patch 0003-Custom-patch-to-support-range-search-params.patch 0004-Custom-patch-to-support-binary-vector.patch PATHS ${CMAKE_CURRENT_SOURCE_DIR}/patches/faiss NO_DEFAULT_PATH)
+# Define list of patch files
+set(PATCH_FILE_LIST)
+list(APPEND PATCH_FILE_LIST "${CMAKE_CURRENT_SOURCE_DIR}/patches/faiss/0001-Custom-patch-to-support-multi-vector.patch")
+list(APPEND PATCH_FILE_LIST "${CMAKE_CURRENT_SOURCE_DIR}/patches/faiss/0002-Enable-precomp-table-to-be-shared-ivfpq.patch")
+list(APPEND PATCH_FILE_LIST "${CMAKE_CURRENT_SOURCE_DIR}/patches/faiss/0003-Custom-patch-to-support-range-search-params.patch")
+list(APPEND PATCH_FILE_LIST "${CMAKE_CURRENT_SOURCE_DIR}/patches/faiss/0004-Custom-patch-to-support-binary-vector.patch")
 
-# If it exists, apply patches
-if (EXISTS ${PATCH_FILE})
-    message(STATUS "Applying custom patches.")
-    execute_process(COMMAND git ${GIT_PATCH_COMMAND} --3way --ignore-space-change --ignore-whitespace ${CMAKE_CURRENT_SOURCE_DIR}/patches/faiss/0001-Custom-patch-to-support-multi-vector.patch WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/external/faiss ERROR_VARIABLE ERROR_MSG RESULT_VARIABLE RESULT_CODE)
-    execute_process(COMMAND git ${GIT_PATCH_COMMAND} --3way --ignore-space-change --ignore-whitespace ${CMAKE_CURRENT_SOURCE_DIR}/patches/faiss/0002-Enable-precomp-table-to-be-shared-ivfpq.patch WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/external/faiss ERROR_VARIABLE ERROR_MSG RESULT_VARIABLE RESULT_CODE)
-    execute_process(COMMAND git ${GIT_PATCH_COMMAND} --3way --ignore-space-change --ignore-whitespace ${CMAKE_CURRENT_SOURCE_DIR}/patches/faiss/0003-Custom-patch-to-support-range-search-params.patch WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/external/faiss ERROR_VARIABLE ERROR_MSG RESULT_VARIABLE RESULT_CODE)
-    execute_process(COMMAND git ${GIT_PATCH_COMMAND} --3way --ignore-space-change --ignore-whitespace ${CMAKE_CURRENT_SOURCE_DIR}/patches/faiss/0004-Custom-patch-to-support-binary-vector.patch WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/external/faiss ERROR_VARIABLE ERROR_MSG RESULT_VARIABLE RESULT_CODE)
+# Get patch id of the last commit
+execute_process(COMMAND sh -c "git --no-pager show HEAD | git patch-id --stable" OUTPUT_VARIABLE PATCH_ID_OUTPUT_FROM_COMMIT WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/external/faiss)
+string(REPLACE " " ";" PATCH_ID_LIST_FROM_COMMIT ${PATCH_ID_OUTPUT_FROM_COMMIT})
+list(GET PATCH_ID_LIST_FROM_COMMIT 0 PATCH_ID_FROM_COMMIT)
+
+# Find all patch files need to apply
+list(SORT PATCH_FILE_LIST ORDER DESCENDING)
+set(PATCH_FILES_TO_APPLY)
+foreach(PATCH_FILE IN LISTS PATCH_FILE_LIST)
+    # Get patch id of a patch file
+    execute_process(COMMAND sh -c "cat ${PATCH_FILE} | git patch-id --stable" OUTPUT_VARIABLE PATCH_ID_OUTPUT)
+    string(REPLACE " " ";" PATCH_ID_LIST ${PATCH_ID_OUTPUT})
+    list(GET PATCH_ID_LIST 0 PATCH_ID)
+
+    # Add the file to patch list if patch id does not match
+    if (${PATCH_ID} STREQUAL ${PATCH_ID_FROM_COMMIT})
+        break()
+    else()
+        list(APPEND PATCH_FILES_TO_APPLY ${PATCH_FILE})
+    endif()
+endforeach()
+
+# Apply patch files
+list(SORT PATCH_FILES_TO_APPLY)
+foreach(PATCH_FILE IN LISTS PATCH_FILES_TO_APPLY)
+    message(STATUS "Applying patch of ${PATCH_FILE}")
+    execute_process(COMMAND git ${GIT_PATCH_COMMAND} --3way --ignore-space-change --ignore-whitespace ${PATCH_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/external/faiss ERROR_VARIABLE ERROR_MSG RESULT_VARIABLE RESULT_CODE)
     if(RESULT_CODE)
         message(FATAL_ERROR "Failed to apply patch:\n${ERROR_MSG}")
     endif()
-endif()
+endforeach()
 
 if (${CMAKE_SYSTEM_NAME} STREQUAL Darwin)
     if(CMAKE_C_COMPILER_ID MATCHES "Clang\$")
diff --git a/jni/cmake/init-nmslib.cmake b/jni/cmake/init-nmslib.cmake
index 387dce6bc..56c52bb69 100644
--- a/jni/cmake/init-nmslib.cmake
+++ b/jni/cmake/init-nmslib.cmake
@@ -12,18 +12,41 @@ if (NOT EXISTS ${NMS_REPO_DIR})
     execute_process(COMMAND git submodule update --init -- external/nmslib WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
 endif ()
 
-# Check if patch exist, this is to skip git apply during CI build. See CI.yml with ubuntu.
-find_path(PATCH_FILE NAMES 0001-Initialize-maxlevel-during-add-from-enterpoint-level.patch 0002-Adds-ability-to-pass-ef-parameter-in-the-query-for-h.patch PATHS ${CMAKE_CURRENT_SOURCE_DIR}/patches/nmslib NO_DEFAULT_PATH)
+# Define list of patch files
+set(PATCH_FILE_LIST)
+list(APPEND PATCH_FILE_LIST "${CMAKE_CURRENT_SOURCE_DIR}/patches/nmslib/0001-Initialize-maxlevel-during-add-from-enterpoint-level.patch")
+list(APPEND PATCH_FILE_LIST "${CMAKE_CURRENT_SOURCE_DIR}/patches/nmslib/0002-Adds-ability-to-pass-ef-parameter-in-the-query-for-h.patch")
 
-# If it exists, apply patches
-if (EXISTS ${PATCH_FILE})
-    message(STATUS "Applying custom patches.")
-    execute_process(COMMAND git ${GIT_PATCH_COMMAND} --3way --ignore-space-change --ignore-whitespace ${CMAKE_CURRENT_SOURCE_DIR}/patches/nmslib/0001-Initialize-maxlevel-during-add-from-enterpoint-level.patch WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/external/nmslib ERROR_VARIABLE ERROR_MSG RESULT_VARIABLE RESULT_CODE)
-    execute_process(COMMAND git ${GIT_PATCH_COMMAND} --3way --ignore-space-change --ignore-whitespace ${CMAKE_CURRENT_SOURCE_DIR}/patches/nmslib/0002-Adds-ability-to-pass-ef-parameter-in-the-query-for-h.patch WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/external/nmslib ERROR_VARIABLE ERROR_MSG RESULT_VARIABLE RESULT_CODE)
+# Get patch id of the last commit
+execute_process(COMMAND sh -c "git --no-pager show HEAD | git patch-id --stable" OUTPUT_VARIABLE PATCH_ID_OUTPUT_FROM_COMMIT WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/external/nmslib)
+string(REPLACE " " ";" PATCH_ID_LIST_FROM_COMMIT ${PATCH_ID_OUTPUT_FROM_COMMIT})
+list(GET PATCH_ID_LIST_FROM_COMMIT 0 PATCH_ID_FROM_COMMIT)
 
+# Find all patch files need to apply
+list(SORT PATCH_FILE_LIST ORDER DESCENDING)
+set(PATCH_FILES_TO_APPLY)
+foreach(PATCH_FILE IN LISTS PATCH_FILE_LIST)
+    # Get patch id of a patch file
+    execute_process(COMMAND sh -c "cat ${PATCH_FILE} | git patch-id --stable" OUTPUT_VARIABLE PATCH_ID_OUTPUT)
+    string(REPLACE " " ";" PATCH_ID_LIST ${PATCH_ID_OUTPUT})
+    list(GET PATCH_ID_LIST 0 PATCH_ID)
+
+    # Add the file to patch list if patch id does not match
+    if (${PATCH_ID} STREQUAL ${PATCH_ID_FROM_COMMIT})
+        break()
+    else()
+        list(APPEND PATCH_FILES_TO_APPLY ${PATCH_FILE})
+    endif()
+endforeach()
+
+# Apply patch files
+list(SORT PATCH_FILES_TO_APPLY)
+foreach(PATCH_FILE IN LISTS PATCH_FILES_TO_APPLY)
+    message(STATUS "Applying patch of ${PATCH_FILE}")
+    execute_process(COMMAND git ${GIT_PATCH_COMMAND} --3way --ignore-space-change --ignore-whitespace ${PATCH_FILE} WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/external/nmslib ERROR_VARIABLE ERROR_MSG RESULT_VARIABLE RESULT_CODE)
     if(RESULT_CODE)
         message(FATAL_ERROR "Failed to apply patch:\n${ERROR_MSG}")
     endif()
-endif()
+endforeach()
 
 add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/external/nmslib/similarity_search)