diff --git a/lib/spack/spack/cmd/common/arguments.py b/lib/spack/spack/cmd/common/arguments.py
index 5e3027babe2..e11a47162a6 100644
--- a/lib/spack/spack/cmd/common/arguments.py
+++ b/lib/spack/spack/cmd/common/arguments.py
@@ -529,6 +529,7 @@ def __call__(self, parser, namespace, values, option_string):
         # the const from the constructor or a value from the CLI.
         # Note that this is only called if the argument is actually
         # specified on the command line.
+        spack.config.CONFIG.ensure_scope_ordering()
         spack.config.set(self.config_path, self.const, scope="command_line")
 
 
diff --git a/lib/spack/spack/config.py b/lib/spack/spack/config.py
index 9bf7675ac20..4252e18fc7b 100644
--- a/lib/spack/spack/config.py
+++ b/lib/spack/spack/config.py
@@ -431,6 +431,19 @@ def ensure_unwrapped(self) -> "Configuration":
         """Ensure we unwrap this object from any dynamic wrapper (like Singleton)"""
         return self
 
+    def highest(self) -> ConfigScope:
+        """Scope with highest precedence"""
+        return next(reversed(self.scopes.values()))  # type: ignore
+
+    @_config_mutator
+    def ensure_scope_ordering(self):
+        """Ensure that scope order matches documented precedent"""
+        # FIXME: We also need to consider that custom configurations and other orderings
+        # may not be preserved correctly
+        if "command_line" in self.scopes:
+            # TODO (when dropping python 3.6): self.scopes.move_to_end
+            self.scopes["command_line"] = self.remove_scope("command_line")
+
     @_config_mutator
     def push_scope(self, scope: ConfigScope) -> None:
         """Add a higher precedence scope to the Configuration."""
diff --git a/lib/spack/spack/environment/environment.py b/lib/spack/spack/environment/environment.py
index 75d2e3d1f30..535afac96e2 100644
--- a/lib/spack/spack/environment/environment.py
+++ b/lib/spack/spack/environment/environment.py
@@ -3043,11 +3043,13 @@ def prepare_config_scope(self) -> None:
         """Add the manifest's scopes to the global configuration search path."""
         for scope in self.env_config_scopes:
             spack.config.CONFIG.push_scope(scope)
+        spack.config.CONFIG.ensure_scope_ordering()
 
     def deactivate_config_scope(self) -> None:
         """Remove any of the manifest's scopes from the global config path."""
         for scope in self.env_config_scopes:
             spack.config.CONFIG.remove_scope(scope.name)
+        spack.config.CONFIG.ensure_scope_ordering()
 
     @contextlib.contextmanager
     def use_config(self):
diff --git a/lib/spack/spack/test/config.py b/lib/spack/spack/test/config.py
index f0d4b0b7b0b..d8642df9bd5 100644
--- a/lib/spack/spack/test/config.py
+++ b/lib/spack/spack/test/config.py
@@ -1441,3 +1441,30 @@ def test_config_path_dsl(path, it_should_work, expected_parsed):
     else:
         with pytest.raises(ValueError):
             spack.config.ConfigPath._validate(path)
+
+
+@pytest.mark.regression("48254")
+def test_env_activation_preserves_config_scopes(mutable_mock_env_path):
+    """Check that the "command_line" scope remains the highest priority scope, when we activate,
+    or deactivate, environments.
+    """
+    expected_cl_scope = spack.config.CONFIG.highest()
+    assert expected_cl_scope.name == "command_line"
+
+    # Creating an environment pushes a new scope
+    ev.create("test")
+    with ev.read("test"):
+        assert spack.config.CONFIG.highest() == expected_cl_scope
+
+        # No active environment pops the scope
+        with ev.no_active_environment():
+            assert spack.config.CONFIG.highest() == expected_cl_scope
+        assert spack.config.CONFIG.highest() == expected_cl_scope
+
+        # Switch the environment to another one
+        ev.create("test-2")
+        with ev.read("test-2"):
+            assert spack.config.CONFIG.highest() == expected_cl_scope
+        assert spack.config.CONFIG.highest() == expected_cl_scope
+
+    assert spack.config.CONFIG.highest() == expected_cl_scope