diff --git a/dev/vcpkg/env.sh b/dev/vcpkg/env.sh
index 91aaa6a7d267..009e9faba2ac 100755
--- a/dev/vcpkg/env.sh
+++ b/dev/vcpkg/env.sh
@@ -7,25 +7,34 @@ if [ -z "${BASH_SOURCE[0]}" ] || [ "$0" == "${BASH_SOURCE[0]}" ]; then
 fi
 
 SCRIPT_ROOT="$(realpath "$(dirname "${BASH_SOURCE[0]}")")"
-init_vcpkg_env=$("${SCRIPT_ROOT}/init.sh" $@)
-eval "$init_vcpkg_env"
 
 export VCPKG_ROOT="$SCRIPT_ROOT/.vcpkg"
 export VCPKG="$SCRIPT_ROOT/.vcpkg/vcpkg"
 export VCPKG_TRIPLET=x64-linux-avx
 export VCPKG_TRIPLET_INSTALL_DIR=${SCRIPT_ROOT}/vcpkg_installed/${VCPKG_TRIPLET}
-export EXPORT_TOOLS_PATH="${VCPKG_TRIPLET_INSTALL_DIR}/tools/protobuf"
 
-if [ "\${GLUTEN_VCPKG_ENABLED:-}" != "${VCPKG_ROOT}" ]; then
+${SCRIPT_ROOT}/init.sh "$@"
+
+if [ "${GLUTEN_VCPKG_ENABLED:-}" != "${VCPKG_ROOT}" ]; then
+    EXPORT_TOOLS_PATH="${VCPKG_TRIPLET_INSTALL_DIR}/tools/protobuf"
+    # The scripts depends on environment $CMAKE_TOOLCHAIN_FILE, which requires
+    # cmake >= 3.21. If system cmake < 3.25, vcpkg will download latest cmake. We
+    # can use vcpkg's internal cmake if we find it.
+    VCPKG_CMAKE_BIN_DIR=$(echo "${VCPKG_ROOT}"/downloads/tools/cmake-*/cmake-*/bin)
+    if [ -f "$VCPKG_CMAKE_BIN_DIR/cmake" ]; then
+        EXPORT_TOOLS_PATH="${VCPKG_CMAKE_BIN_DIR}:${EXPORT_TOOLS_PATH}"
+    fi
+    EXPORT_TOOLS_PATH=${EXPORT_TOOLS_PATH/%:/}
+
     export VCPKG_ROOT=${VCPKG_ROOT}
     export VCPKG_MANIFEST_DIR=${SCRIPT_ROOT}
     export VCPKG_TRIPLET=${VCPKG_TRIPLET}
 
     export CMAKE_TOOLCHAIN_FILE=${SCRIPT_ROOT}/toolchain.cmake
-    export PKG_CONFIG_PATH=${VCPKG_TRIPLET_INSTALL_DIR}/lib/pkgconfig:${VCPKG_TRIPLET_INSTALL_DIR}/share/pkgconfig:\${PKG_CONFIG_PATH:-}
+    export PKG_CONFIG_PATH=${VCPKG_TRIPLET_INSTALL_DIR}/lib/pkgconfig:${VCPKG_TRIPLET_INSTALL_DIR}/share/pkgconfig:${PKG_CONFIG_PATH:-}
     export PATH="${EXPORT_TOOLS_PATH}:$PATH"
 
     export GLUTEN_VCPKG_ENABLED=${VCPKG_ROOT}
 else
-    echo "Gluten's vcpkg environment is enabled" >&2
+    echo "Gluten's vcpkg environment is already enabled" >&2
 fi
diff --git a/dev/vcpkg/init.sh b/dev/vcpkg/init.sh
index 9beaa19526fe..bae1a8ad32eb 100755
--- a/dev/vcpkg/init.sh
+++ b/dev/vcpkg/init.sh
@@ -2,8 +2,6 @@
 
 set -e
 
-exec 3>&1 >&2
-
 BUILD_TESTS=OFF
 ENABLE_S3=OFF
 ENABLE_GCS=OFF
@@ -39,11 +37,19 @@ for arg in "$@"; do
   esac
 done
 
-export SCRIPT_ROOT="$(realpath "$(dirname "$0")")"
-export VCPKG_ROOT="$SCRIPT_ROOT/.vcpkg"
-export VCPKG="$SCRIPT_ROOT/.vcpkg/vcpkg"
-VCPKG_TRIPLET=x64-linux-avx
+require_set() {
+  if [ -z "${!1}" ]; then
+    echo "Required variable $1 not found!"
+    exit 1
+  fi
+}
+
+require_set "VCPKG_ROOT"
+require_set "VCPKG"
+require_set "VCPKG_TRIPLET"
+require_set "VCPKG_TRIPLET_INSTALL_DIR"
 
+SCRIPT_ROOT="$(realpath "$(dirname "$0")")"
 cd "$SCRIPT_ROOT"
 
 if [ ! -d "$VCPKG_ROOT" ] || [ -z "$(ls "$VCPKG_ROOT")" ]; then
@@ -75,19 +81,6 @@ fi
 $VCPKG install --no-print-usage \
     --triplet="${VCPKG_TRIPLET}" --host-triplet="${VCPKG_TRIPLET}" ${EXTRA_FEATURES}
 
-export VCPKG_TRIPLET_INSTALL_DIR=${SCRIPT_ROOT}/vcpkg_installed/${VCPKG_TRIPLET}
-EXPORT_TOOLS_PATH="${VCPKG_TRIPLET_INSTALL_DIR}/tools/protobuf"
-
-# This scripts depends on environment $CMAKE_TOOLCHAIN_FILE, which requires
-# cmake >= 3.21. If system cmake < 3.25, vcpkg will download latest cmake. We
-# can use vcpkg's internal cmake if we find it.
-VCPKG_CMAKE_BIN_DIR=$(echo "${VCPKG_ROOT}"/downloads/tools/cmake-*/cmake-*/bin)
-if [ -f "$VCPKG_CMAKE_BIN_DIR/cmake" ]; then
-    EXPORT_TOOLS_PATH="${VCPKG_CMAKE_BIN_DIR}:${EXPORT_TOOLS_PATH}"
-fi
-
-export EXPORT_TOOLS_PATH=${EXPORT_TOOLS_PATH/%:/}
-
 # For fixing a build error like below when gluten's build type is Debug:
 # No rule to make target '/root/gluten/dev/vcpkg/vcpkg_installed/x64-linux-avx/debug/lib/libz.a',
 # needed by 'releases/libvelox.so'
diff --git a/dev/vcpkg/toolchain.cmake b/dev/vcpkg/toolchain.cmake
index 21ff9090fb9e..10d156c1b040 100644
--- a/dev/vcpkg/toolchain.cmake
+++ b/dev/vcpkg/toolchain.cmake
@@ -3,11 +3,15 @@
 
 set(ENABLE_GLUTEN_VCPKG ON)
 
-# If this arg is set, `vcpkg install` will be executed according
-# to the manifest file exists in this given path, i.e., vcpkg.json,
-# which will not respect our setting for extra features through
-# `--x-feature`.
-#set(VCPKG_MANIFEST_DIR $ENV{VCPKG_MANIFEST_DIR})
+# Force the use of VCPKG classic mode to avoid reinstalling vcpkg features during
+# different CMake sub-projects. Which means, the features installed by `vcpkg install`
+# in script `init.sh` will be used across all CMake sub-projects.
+#
+# Reference: https://learn.microsoft.com/en-us/vcpkg/users/buildsystems/cmake-integration
+#
+# Note: "CACHE BOOL" is required to make this successfully override the option defined in
+# vcpkg.cmake.
+set(VCPKG_MANIFEST_MODE OFF CACHE BOOL "Use manifest mode, as opposed to classic mode." FORCE)
 
 set(VCPKG_TARGET_TRIPLET $ENV{VCPKG_TRIPLET})
 set(VCPKG_HOST_TRIPLET $ENV{VCPKG_TRIPLET})