diff --git a/interfaces/cython/SConscript b/interfaces/cython/SConscript
index 7b7839e4202..3388bdcd1b1 100644
--- a/interfaces/cython/SConscript
+++ b/interfaces/cython/SConscript
@@ -36,9 +36,12 @@ script = """\
 from sysconfig import *
 import numpy
 import json
+import site
 vars = get_config_vars()
 vars["plat"] = get_platform()
 vars["numpy_include"] = numpy.get_include()
+vars["site_packages"] = site.getsitepackages()
+vars["user_site_packages"] = site.getusersitepackages()
 print(json.dumps(vars))
 """
 info = json.loads(get_command_output(localenv["python_cmd"], "-c", script))
@@ -50,6 +53,8 @@ py_version_short = parse_version(info["py_version_short"])
 py_version_full = parse_version(info["py_version"])
 py_version_nodot = info["py_version_nodot"]
 numpy_include = info["numpy_include"]
+site_packages = info["site_packages"]
+user_site_packages = info["user_site_packages"]
 localenv.Prepend(CPPPATH=[Dir('#include'), inc, numpy_include])
 localenv.Prepend(LIBS=localenv['cantera_libs'])
 
@@ -137,6 +142,27 @@ elif not env["default_prefix"]:
     install_cmd.append(f"--prefix={env['prefix']}")
     python_prefix = env["prefix"]
 
+# Check for existing Python module installation. Allow pip to remove an existing
+# installation only we're installing to the same location. Also disable uninstallation
+# if we're installing to a staging directory.
+if env["stage_dir"]:
+    install_cmd.append("--ignore-installed")
+else:
+    info = get_command_output(localenv["python_cmd"], "-m", "pip", "show", "cantera",
+                              ignore_errors=True)
+
+    if user_install:
+        test_prefix = Path(user_site_packages).parents[2]
+    elif python_prefix is None:
+        test_prefix = Path(site_packages).parents[2]
+    else:
+        test_prefix = Path(python_prefix)
+
+    match = re.search(r"Location: (.*)\n", info, re.MULTILINE)
+    existing_prefix = Path(match.group(1)).parents[2] if match else None
+    if existing_prefix and existing_prefix != test_prefix:
+        install_cmd.append("--ignore-installed")
+
 if env["stage_dir"]:
     # Get the absolute path to the stage directory. If the stage directory is a relative
     # path, consider it to be relative to the root of the Cantera source directory.
diff --git a/site_scons/buildutils.py b/site_scons/buildutils.py
index 05dc82f3a08..f47707c4eed 100644
--- a/site_scons/buildutils.py
+++ b/site_scons/buildutils.py
@@ -1188,7 +1188,7 @@ def our_spawn(sh: str, escape: str, cmd: str, args: str, environ: "Dict[str, str
     return our_spawn
 
 
-def get_command_output(cmd: str, *args: str):
+def get_command_output(cmd: str, *args: str, ignore_errors=False):
     """
     Run a command with arguments and return its output.
     """
@@ -1196,12 +1196,16 @@ def get_command_output(cmd: str, *args: str):
     if "PYTHONHOME" in environ:
         # Can cause problems when trying to run a different Python interpreter
         del environ["PYTHONHOME"]
+    kwargs = {}
+    if ignore_errors:
+        kwargs["stderr"] = subprocess.DEVNULL
     data = subprocess.run(
         [cmd] + list(args),
         env=environ,
         stdout=subprocess.PIPE,
         universal_newlines=True,
-        check=True,
+        check=not ignore_errors,
+        **kwargs,
     )
     return data.stdout.strip()