diff --git a/ci/scripts/java_jni_macos_build.sh b/ci/scripts/java_jni_macos_build.sh
index b0fc52e42cdaa..51a2d4d1dee14 100755
--- a/ci/scripts/java_jni_macos_build.sh
+++ b/ci/scripts/java_jni_macos_build.sh
@@ -82,7 +82,7 @@ cmake \
   -DARROW_S3=${ARROW_S3} \
   -DARROW_USE_CCACHE=${ARROW_USE_CCACHE} \
   -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} \
-  -DCMAKE_INSTALL_LIBDIR=lib \
+  -DCMAKE_ARCH_DIR=${normalized_arch} \
   -DCMAKE_INSTALL_PREFIX=${install_dir} \
   -DCMAKE_UNITY_BUILD=${CMAKE_UNITY_BUILD} \
   -DGTest_SOURCE=BUNDLED \
diff --git a/ci/scripts/java_jni_manylinux_build.sh b/ci/scripts/java_jni_manylinux_build.sh
index a15eb89f6586b..9be129e08c4c1 100755
--- a/ci/scripts/java_jni_manylinux_build.sh
+++ b/ci/scripts/java_jni_manylinux_build.sh
@@ -91,7 +91,7 @@ cmake \
   -DARROW_S3=${ARROW_S3} \
   -DARROW_USE_CCACHE=${ARROW_USE_CCACHE} \
   -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} \
-  -DCMAKE_INSTALL_LIBDIR=lib \
+  -DCMAKE_ARCH_DIR=${normalized_arch} \
   -DCMAKE_INSTALL_PREFIX=${ARROW_HOME} \
   -DCMAKE_UNITY_BUILD=${CMAKE_UNITY_BUILD} \
   -DGTest_SOURCE=BUNDLED \
diff --git a/ci/scripts/java_jni_windows_build.sh b/ci/scripts/java_jni_windows_build.sh
index 778ee9696790e..e56827ce910ce 100755
--- a/ci/scripts/java_jni_windows_build.sh
+++ b/ci/scripts/java_jni_windows_build.sh
@@ -72,7 +72,7 @@ cmake \
   -DARROW_WITH_SNAPPY=ON \
   -DARROW_WITH_ZSTD=ON \
   -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} \
-  -DCMAKE_INSTALL_LIBDIR=lib \
+  -DCMAKE_ARCH_DIR=x86_64 \
   -DCMAKE_INSTALL_PREFIX=${install_dir} \
   -DCMAKE_UNITY_BUILD=${CMAKE_UNITY_BUILD} \
   -GNinja \