diff --git a/pyodide_build/pywasmcross.py b/pyodide_build/pywasmcross.py
index 52aa6effd..561d3f738 100755
--- a/pyodide_build/pywasmcross.py
+++ b/pyodide_build/pywasmcross.py
@@ -264,12 +264,26 @@ def handle_command(line, args, dryrun=False):
     elif new_args[0] == "em++":
         new_args.extend(args.cflags.split() + args.cxxflags.split())
 
+    optflags_valid = [f"-O{tok}" for tok in "01234sz"]
+    optflag = None
+    # Identify the optflag (e.g. -O3) in cflags/cxxflags/ldflags. Last one has
+    # priority.
+    for arg in new_args[::-1]:
+        if arg in optflags_valid:
+            optflag = arg
+            break
+
     lapack_dir = None
 
     used_libs = set()
 
     # Go through and adjust arguments
     for arg in line[1:]:
+        if arg in optflags_valid and optflag is not None and arg != optflag:
+            # There are multiple contradictory optflags provided, use the one
+            # from cflags/cxxflags/ldflags
+            continue
+
         if arg.startswith("-I"):
             if (
                 str(Path(arg[2:]).resolve()).startswith(sys.prefix + "/include/python")
diff --git a/pyodide_build/tests/test_pywasmcross.py b/pyodide_build/tests/test_pywasmcross.py
index d2f1d5c1a..c6411862b 100644
--- a/pyodide_build/tests/test_pywasmcross.py
+++ b/pyodide_build/tests/test_pywasmcross.py
@@ -1,7 +1,9 @@
-from collections import namedtuple
 from pathlib import Path
 import sys
 import argparse
+from dataclasses import dataclass
+
+import pytest
 
 sys.path.append(str(Path(__file__).parents[2]))
 
@@ -10,6 +12,18 @@ from pyodide_build.pywasmcross import f2c  # noqa: E402
 from pyodide_build.pywasmcross import make_parser
 
 
+@dataclass
+class BuildArgs:
+    """An object to hold build arguments"""
+
+    cflags: str = ""
+    cxxflags: str = ""
+    ldflags: str = ""
+    host: str = ""
+    replace_libs: str = ""
+    install_dir: str = ""
+
+
 def _args_wrapper(func):
     """Convert function to take as input / return a string instead of a
     list of arguments
@@ -33,12 +47,7 @@ f2c_wrap = _args_wrapper(f2c)
 
 
 def test_handle_command():
-    Args = namedtuple(
-        "args", ["cflags", "cxxflags", "ldflags", "host", "replace_libs", "install_dir"]
-    )
-    args = Args(
-        cflags="", cxxflags="", ldflags="", host="", replace_libs="", install_dir=""
-    )
+    args = BuildArgs()
     assert handle_command_wrap("gcc -print-multiarch", args) is None
     assert handle_command_wrap("gcc test.c", args) == "emcc test.c"
     assert (
@@ -47,13 +56,10 @@ def test_handle_command():
     )
 
     # check cxxflags injection and cpp detection
-    args = Args(
+    args = BuildArgs(
         cflags="-I./lib2",
         cxxflags="-std=c++11",
         ldflags="-lm",
-        host="",
-        replace_libs="",
-        install_dir="",
     )
     assert (
         handle_command_wrap("gcc -I./lib1 test.cpp -o test.o", args)
@@ -61,7 +67,7 @@ def test_handle_command():
     )
 
     # check ldflags injection
-    args = Args(
+    args = BuildArgs(
         cflags="", cxxflags="", ldflags="-lm", host="", replace_libs="", install_dir=""
     )
     assert (
@@ -70,13 +76,8 @@ def test_handle_command():
     )
 
     # check library replacement and removal of double libraries
-    args = Args(
-        cflags="",
-        cxxflags="",
-        ldflags="",
-        host="",
+    args = BuildArgs(
         replace_libs="bob=fred",
-        install_dir="",
     )
     assert (
         handle_command_wrap("gcc -shared test.o -lbob -ljim -ljim -o test.so", args)
@@ -87,6 +88,25 @@ def test_handle_command():
     assert handle_command_wrap("gcc /usr/file.c", args) is None
 
 
+@pytest.mark.parametrize(
+    "in_ext, out_ext, executable, flag_name",
+    [
+        (".c", ".o", "emcc", "cflags"),
+        (".cpp", ".o", "em++", "cxxflags"),
+        (".c", ".so", "emcc", "ldflags"),
+    ],
+)
+def test_handle_command_optflags(in_ext, out_ext, executable, flag_name):
+    # Make sure that when multiple optflags are present those in cflags,
+    # cxxflags, or ldflags has priority
+
+    args = BuildArgs(**{flag_name: "-Oz"})
+    assert (
+        handle_command_wrap(f"gcc -O3 test.{in_ext} -o test.{out_ext}", args)
+        == f"{executable} -Oz test.{in_ext} -o test.{out_ext}"
+    )
+
+
 def test_f2c():
     assert f2c_wrap("gfortran test.f") == "gfortran test.c"
     assert f2c_wrap("gcc test.c") is None
@@ -98,12 +118,7 @@ def test_f2c():
 
 
 def test_conda_compiler_compat():
-    Args = namedtuple(
-        "args", ["cflags", "cxxflags", "ldflags", "host", "replace_libs", "install_dir"]
-    )
-    args = Args(
-        cflags="", cxxflags="", ldflags="", host="", replace_libs="", install_dir=""
-    )
+    args = BuildArgs()
     assert handle_command_wrap(
         "gcc -shared -c test.o -B /compiler_compat -o test.so", args
     ) == ("emcc -c test.o -o test.so")