diff --git a/eng/common/cross/build-rootfs.sh b/eng/common/cross/build-rootfs.sh
old mode 100755
new mode 100644
index 032f5f19373..737a61aa4b3
--- a/eng/common/cross/build-rootfs.sh
+++ b/eng/common/cross/build-rootfs.sh
@@ -458,12 +458,12 @@ elif [[ "$__CodeName" == "haiku" ]]; then
 
     # Setup the sysroot
     echo "Setting up sysroot and extracting needed packages"
-    mkdir -p "$__RootfsDir/boot/system"
+    mkdir -p "$__RootfsDir"
     for file in "$__RootfsDir/generated/objects/haiku/x86_64/packaging/packages/"*.hpkg; do
-        "$__RootfsDir/generated/objects/linux/x86_64/release/tools/package/package" extract -C "$__RootfsDir/boot/system" "$file"
+        "$__RootfsDir/generated/objects/linux/x86_64/release/tools/package/package" extract -C "$__RootfsDir" "$file"
     done
     for file in "$__RootfsDir/generated/download/"*.hpkg; do
-        "$__RootfsDir/generated/objects/linux/x86_64/release/tools/package/package" extract -C "$__RootfsDir/boot/system" "$file"
+        "$__RootfsDir/generated/objects/linux/x86_64/release/tools/package/package" extract -C "$__RootfsDir" "$file"
     done
 
     # Cleaning up temporary files
diff --git a/eng/common/cross/toolchain.cmake b/eng/common/cross/toolchain.cmake
index 561576be97c..9cdba0fda50 100644
--- a/eng/common/cross/toolchain.cmake
+++ b/eng/common/cross/toolchain.cmake
@@ -7,7 +7,7 @@ if(EXISTS ${CROSS_ROOTFS}/bin/freebsd-version)
 elseif(EXISTS ${CROSS_ROOTFS}/usr/platform/i86pc)
   set(CMAKE_SYSTEM_NAME SunOS)
   set(ILLUMOS 1)
-elseif(EXISTS ${CROSS_ROOTFS}/boot/system/develop/headers/config/HaikuConfig.h)
+elseif(EXISTS ${CROSS_ROOTFS}/develop/headers/config/HaikuConfig.h)
   set(CMAKE_SYSTEM_NAME Haiku)
 else()
   set(CMAKE_SYSTEM_NAME Linux)