diff --git a/tools/pybind11Common.cmake b/tools/pybind11Common.cmake
index e4ff1e4080..ef66fb5932 100644
--- a/tools/pybind11Common.cmake
+++ b/tools/pybind11Common.cmake
@@ -292,21 +292,24 @@ function(_pybind11_generate_lto target prefer_thin_lto)
       set(cxx_append ";-fno-fat-lto-objects")
     endif()
 
-    if(CMAKE_SYSTEM_PROCESSOR MATCHES "ppc64le" OR CMAKE_SYSTEM_PROCESSOR MATCHES "mips64")
-      set(NO_FLTO_ARCH TRUE)
+    if(prefer_thin_lto)
+      set(thin "=thin")
     else()
-      set(NO_FLTO_ARCH FALSE)
+      set(thin "")
     endif()
 
-    if(CMAKE_CXX_COMPILER_ID MATCHES "Clang"
-       AND prefer_thin_lto
-       AND NOT NO_FLTO_ARCH)
+    if(CMAKE_SYSTEM_PROCESSOR MATCHES "ppc64le" OR CMAKE_SYSTEM_PROCESSOR MATCHES "mips64")
+      # Do nothing
+    elseif(CMAKE_SYSTEM_PROCESSOR MATCHES emscripten)
+      # This compile is very costly when cross-compiling, so set this without checking
+      set(PYBIND11_LTO_CXX_FLAGS "-flto${thin}${cxx_append}")
+      set(PYBIND11_LTO_LINKER_FLAGS "-flto${thin}${linker_append}")
+    elseif(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
       _pybind11_return_if_cxx_and_linker_flags_work(
-        HAS_FLTO_THIN "-flto=thin${cxx_append}" "-flto=thin${linker_append}"
+        HAS_FLTO_THIN "-flto${thin}${cxx_append}" "-flto=${thin}${linker_append}"
         PYBIND11_LTO_CXX_FLAGS PYBIND11_LTO_LINKER_FLAGS)
     endif()
-
-    if(NOT HAS_FLTO_THIN AND NOT NO_FLTO_ARCH)
+    if(NOT HAS_FLTO_THIN)
       _pybind11_return_if_cxx_and_linker_flags_work(
         HAS_FLTO "-flto${cxx_append}" "-flto${linker_append}" PYBIND11_LTO_CXX_FLAGS
         PYBIND11_LTO_LINKER_FLAGS)