diff --git a/ports/libvpx/0006-gen-vcxproj-ignore-unknown-flags.patch b/ports/libvpx/0006-gen-vcxproj-ignore-unknown-flags.patch
new file mode 100644
index 0000000000..72469ab432
--- /dev/null
+++ b/ports/libvpx/0006-gen-vcxproj-ignore-unknown-flags.patch
@@ -0,0 +1,11 @@
+--- a/build/make/gen_msvs_vcxproj.sh
++++ b/build/make/gen_msvs_vcxproj.sh
+@@ -209,7 +209,7 @@
+         ;;
+         -l*) libs="${libs}${libs:+ }${opt##-l}.lib"
+         ;;
+-        -*) die_unknown $opt
++        -*) : # Ignore unknown flags (e.g. -O3 leaked from GCC CFLAGS)
+         ;;
+         *)
+             # The paths in file_list are fixed outside of the loop.
diff --git a/ports/libvpx/0007-msvc-use-Fo-in-toolchain-probe.patch b/ports/libvpx/0007-msvc-use-Fo-in-toolchain-probe.patch
new file mode 100644
index 0000000000..a249856c2c
--- /dev/null
+++ b/ports/libvpx/0007-msvc-use-Fo-in-toolchain-probe.patch
@@ -0,0 +1,79 @@
+--- a/build/make/configure.sh	2026-05-13 08:17:31.764191365 +0200
++++ b/build/make/configure.sh	2026-05-13 08:18:26.744873378 +0200
+@@ -298,37 +298,71 @@
+   "$@" >>${logfile} 2>&1
+ }
+ 
++# Emit the compiler/linker output flag for the given file.
++# cl.exe (and clang-cl when driven in cl mode) require -Fo<obj> / -Fe<exe> with no separating space;
++# every other compiler uses the GCC-style -o <file>.
++_cc_basename() {
++  local _cc="${1##*/}"
++  _cc="${_cc##*\\}"
++  echo "${_cc%.exe}"
++}
++
++# Convert a path to native Windows form when the compiler is MSVC.
++# MSYS2 temporary paths like /tmp/vpx-conf-1234.o get translated by the MSYS layer to D:\tmp\... which does not exist.
++# cygpath -w produces the real Windows path (e.g. C:\msys64\tmp\...).
++_native_output_path() {
++  case "$(_cc_basename "${1}")" in
++    cl|clang-cl|link) cygpath -w "$2" ;;
++    *)                echo "$2" ;;
++  esac
++}
++
++cc_obj_flag() {
++  case "$(_cc_basename "${CC}")" in
++    cl|clang-cl) echo "-Fo$(_native_output_path "${CC}" "$1")" ;;
++    *)           echo "-o $1" ;;
++  esac
++}
++
++cc_exe_flag() {
++  case "$(_cc_basename "${LD:-${CC}}")" in
++    cl|clang-cl) echo "-Fe$(_native_output_path "${LD:-${CC}}" "$1")" ;;
++    link)        echo "/OUT:$(_native_output_path "${LD:-${CC}}" "$1")" ;;
++    *)           echo "-o $1" ;;
++  esac
++}
++
+ check_cc() {
+   log check_cc "$@"
+   cat >${TMP_C}
+   log_file ${TMP_C}
+-  check_cmd ${CC} ${CFLAGS} "$@" -c -o ${TMP_O} ${TMP_C}
++  check_cmd ${CC} ${CFLAGS} "$@" -c $(cc_obj_flag ${TMP_O}) ${TMP_C}
+ }
+ 
+ check_cxx() {
+   log check_cxx "$@"
+   cat >${TMP_CC}
+   log_file ${TMP_CC}
+-  check_cmd ${CXX} ${CXXFLAGS} "$@" -c -o ${TMP_O} ${TMP_CC}
++  check_cmd ${CXX} ${CXXFLAGS} "$@" -c $(cc_obj_flag ${TMP_O}) ${TMP_CC}
+ }
+ 
+ check_cpp() {
+   log check_cpp "$@"
+   cat > ${TMP_C}
+   log_file ${TMP_C}
+-  check_cmd ${CC} ${CFLAGS} "$@" -E -o ${TMP_O} ${TMP_C}
++  check_cmd ${CC} ${CFLAGS} "$@" -E $(cc_obj_flag ${TMP_O}) ${TMP_C}
+ }
+ 
+ check_ld() {
+   log check_ld "$@"
+   check_cc $@ \
+-    && check_cmd ${LD} ${LDFLAGS} "$@" -o ${TMP_X} ${TMP_O} ${extralibs}
++    && check_cmd ${LD} ${LDFLAGS} "$@" $(cc_exe_flag ${TMP_X}) ${TMP_O} ${extralibs}
+ }
+ 
+ check_lib() {
+   log check_lib "$@"
+   check_cc $@ \
+-    && check_cmd ${LD} ${LDFLAGS} -o ${TMP_X} ${TMP_O} "$@" ${extralibs}
++    && check_cmd ${LD} ${LDFLAGS} $(cc_exe_flag ${TMP_X}) ${TMP_O} "$@" ${extralibs}
+ }
+ 
+ check_header(){
diff --git a/ports/libvpx/portfile.cmake b/ports/libvpx/portfile.cmake
index 6fe2596a97..78af9a1390 100644
--- a/ports/libvpx/portfile.cmake
+++ b/ports/libvpx/portfile.cmake
@@ -8,6 +8,10 @@ vcpkg_from_github(
         0003-add-uwp-v142-and-v143-support.patch
         0004-remove-library-suffixes.patch
         0005-dont-expect-gnu-diff.patch
+        0006-gen-vcxproj-ignore-unknown-flags.patch
+        # Candidate upstream fix: makes configure-time toolchain probes use -Fo/-Fe when CC/LD is cl.exe or clang-cl.
+        # Once upstream picks this up (or once we drop --enable-external-build), the MSVC arm64 SVE workaround below can also be removed.
+        0007-msvc-use-Fo-in-toolchain-probe.patch
 )
 
 if(CMAKE_HOST_WIN32)
@@ -30,6 +34,12 @@ endif()
 if(VCPKG_TARGET_IS_WINDOWS AND NOT VCPKG_TARGET_IS_MINGW)
 
     file(REMOVE_RECURSE "${CURRENT_BUILDTREES_DIR}/${TARGET_TRIPLET}-tmp")
+    # Remove stale vpx-* dist directories from previous builds to avoid picking old artifacts.
+    file(GLOB _vpx_stale_dirs "${CURRENT_BUILDTREES_DIR}/${TARGET_TRIPLET}-rel/vpx-*")
+    if(_vpx_stale_dirs)
+        file(REMOVE_RECURSE ${_vpx_stale_dirs})
+    endif()
+
 
     if(VCPKG_CRT_LINKAGE STREQUAL static)
         set(LIBVPX_CRT_LINKAGE --enable-static-msvcrt)
@@ -68,14 +78,26 @@ if(VCPKG_TARGET_IS_WINDOWS AND NOT VCPKG_TARGET_IS_MINGW)
         set(LIBVPX_TARGET_VS "vs15")
     endif()
 
-    set(OPTIONS "--disable-examples --disable-tools --disable-docs --enable-pic")
+    set(OPTIONS --disable-examples --disable-tools --disable-docs --enable-pic --disable-dependency-tracking)
+
+    # Force VS generation to avoids Unix-style rules that break with cl/ar semantics
+    list(APPEND OPTIONS --enable-external-build)
+
+   # Disable SVE/SVE2 probe to avoids missing `<arm_sve.h>` in pure-MSVC.
+    if(VCPKG_TARGET_ARCHITECTURE STREQUAL arm64)
+        vcpkg_cmake_get_vars(_libvpx_cmake_vars_file)
+        include("${_libvpx_cmake_vars_file}")
+        if(VCPKG_DETECTED_CMAKE_C_COMPILER_ID STREQUAL "MSVC")
+            list(APPEND OPTIONS --disable-sve --disable-sve2)
+        endif()
+    endif()
 
     if("realtime" IN_LIST FEATURES)
-        set(OPTIONS "${OPTIONS} --enable-realtime-only")
+        list(APPEND OPTIONS --enable-realtime-only)
     endif()
 
     if("highbitdepth" IN_LIST FEATURES)
-        set(OPTIONS "${OPTIONS} --enable-vp9-highbitdepth")
+        list(APPEND OPTIONS --enable-vp9-highbitdepth)
     endif()
 
     message(STATUS "Generating makefile")
@@ -103,13 +125,18 @@ if(VCPKG_TARGET_IS_WINDOWS AND NOT VCPKG_TARGET_IS_MINGW)
         PROJECT_SUBPATH vpx.vcxproj
     )
 
-    if (VCPKG_TARGET_ARCHITECTURE STREQUAL arm64)
-        set(LIBVPX_INCLUDE_DIR "${CURRENT_BUILDTREES_DIR}/${TARGET_TRIPLET}-rel/vpx-vp8-vp9-nopost-nodocs-${LIBVPX_TARGET_ARCH}${LIBVPX_CRT_SUFFIX}-${LIBVPX_TARGET_VS}-v${VERSION}/include/vpx")
-    elseif (VCPKG_TARGET_ARCHITECTURE STREQUAL arm)
-        set(LIBVPX_INCLUDE_DIR "${CURRENT_BUILDTREES_DIR}/${TARGET_TRIPLET}-rel/vpx-vp8-vp9-nopost-nomt-nodocs-${LIBVPX_TARGET_ARCH}${LIBVPX_CRT_SUFFIX}-${LIBVPX_TARGET_VS}-v${VERSION}/include/vpx")
-    else()
-        set(LIBVPX_INCLUDE_DIR "${CURRENT_BUILDTREES_DIR}/${TARGET_TRIPLET}-rel/vpx-vp8-vp9-nodocs-${LIBVPX_TARGET_ARCH}${LIBVPX_CRT_SUFFIX}-${LIBVPX_TARGET_VS}-v${VERSION}/include/vpx")
+    # libvpx's make dist creates a directory with the pattern:
+    #   vpx-[CODEC_FEATURES]-[ARCH][CRT]-[VS]-v[VERSION]
+    # GLOB to find the actual directory.
+    file(GLOB LIBVPX_INCLUDE_DIR_CANDIDATES
+        "${CURRENT_BUILDTREES_DIR}/${TARGET_TRIPLET}-rel/vpx-*${LIBVPX_TARGET_ARCH}${LIBVPX_CRT_SUFFIX}-${LIBVPX_TARGET_VS}-v${VERSION}/include/vpx")
+    list(LENGTH LIBVPX_INCLUDE_DIR_CANDIDATES _vpx_n)
+    if(_vpx_n EQUAL 0)
+        message(FATAL_ERROR "libvpx: no dist include directory found under ${CURRENT_BUILDTREES_DIR}/${TARGET_TRIPLET}-rel/")
+    elseif(_vpx_n GREATER 1)
+        message(FATAL_ERROR "libvpx: found ${_vpx_n} candidate dist directories; expected exactly one")
     endif()
+    list(GET LIBVPX_INCLUDE_DIR_CANDIDATES 0 LIBVPX_INCLUDE_DIR)
     file(
         INSTALL
             "${LIBVPX_INCLUDE_DIR}"
diff --git a/ports/libvpx/vcpkg.json b/ports/libvpx/vcpkg.json
index 4f6ef1b5ba..7b0e7e9b18 100644
--- a/ports/libvpx/vcpkg.json
+++ b/ports/libvpx/vcpkg.json
@@ -1,7 +1,7 @@
 {
   "name": "libvpx",
   "version": "1.16.0",
-  "port-version": 1,
+  "port-version": 2,
   "description": "The reference software implementation for the video coding formats VP8 and VP9.",
   "homepage": "https://github.com/webmproject/libvpx",
   "license": "BSD-3-Clause",
diff --git a/versions/baseline.json b/versions/baseline.json
index 28eb5d19ba..527a48bfd3 100644
--- a/versions/baseline.json
+++ b/versions/baseline.json
@@ -5870,7 +5870,7 @@
     },
     "libvpx": {
       "baseline": "1.16.0",
-      "port-version": 1
+      "port-version": 2
     },
     "libwandio": {
       "baseline": "4.2.6-1",
diff --git a/versions/l-/libvpx.json b/versions/l-/libvpx.json
index 2ee996235e..a7760a7f7f 100644
--- a/versions/l-/libvpx.json
+++ b/versions/l-/libvpx.json
@@ -1,5 +1,10 @@
 {
   "versions": [
+    {
+      "git-tree": "6ceb7c67ef2fd1729a37204404ef21fc5647154f",
+      "version": "1.16.0",
+      "port-version": 2
+    },
     {
       "git-tree": "5bd5e772e786f6c6c223e2ad94e5a4de30415246",
       "version": "1.16.0",