diff --git a/src/main/java/com/google/devtools/build/lib/bazel/bzlmod/ModuleFileFunction.java b/src/main/java/com/google/devtools/build/lib/bazel/bzlmod/ModuleFileFunction.java
index 04c5548e046789..44fb113ecad0db 100644
--- a/src/main/java/com/google/devtools/build/lib/bazel/bzlmod/ModuleFileFunction.java
+++ b/src/main/java/com/google/devtools/build/lib/bazel/bzlmod/ModuleFileFunction.java
@@ -630,8 +630,8 @@ private static ModuleThreadContext execModuleFile(
             }
           });
 
-      injectRepos(injectedRepositories, context, thread);
       compiledRootModuleFile.runOnThread(thread);
+      injectRepos(injectedRepositories, context, thread);
     } catch (EvalException e) {
       eventHandler.handle(Event.error(e.getInnermostLocation(), e.getMessageWithStack()));
       throw errorf(Code.BAD_MODULE, "error executing MODULE.bazel file for %s", moduleKey);
diff --git a/src/main/java/com/google/devtools/build/lib/bazel/bzlmod/ModuleThreadContext.java b/src/main/java/com/google/devtools/build/lib/bazel/bzlmod/ModuleThreadContext.java
index eafb8a4829d03f..4f16fc9f6ca9cf 100644
--- a/src/main/java/com/google/devtools/build/lib/bazel/bzlmod/ModuleThreadContext.java
+++ b/src/main/java/com/google/devtools/build/lib/bazel/bzlmod/ModuleThreadContext.java
@@ -108,11 +108,12 @@ Location location() {
   public void addRepoNameUsage(
       String repoName, String how, ImmutableList<StarlarkThread.CallStackEntry> stack)
       throws EvalException {
-    RepoNameUsage collision = repoNameUsages.put(repoName, new RepoNameUsage(how, stack));
+    RepoNameUsage incoming = new RepoNameUsage(how, stack);
+    RepoNameUsage collision = repoNameUsages.put(repoName, incoming);
     if (collision != null) {
       throw Starlark.errorf(
-          "The repo name '%s' is already being used %s at %s",
-          repoName, collision.how(), collision.location());
+          "The repo name '%s' cannot be defined %s at %s as it is already defined %s at %s",
+          repoName, incoming.how(), incoming.location(), collision.how(), collision.location());
     }
   }
 
diff --git a/src/test/java/com/google/devtools/build/lib/bazel/bzlmod/ModuleFileFunctionTest.java b/src/test/java/com/google/devtools/build/lib/bazel/bzlmod/ModuleFileFunctionTest.java
index 4f361dc8cdac9f..94b4ffca99d6be 100644
--- a/src/test/java/com/google/devtools/build/lib/bazel/bzlmod/ModuleFileFunctionTest.java
+++ b/src/test/java/com/google/devtools/build/lib/bazel/bzlmod/ModuleFileFunctionTest.java
@@ -522,7 +522,8 @@ public void testRootModule_include_bad_repoNameCollision() throws Exception {
         evaluator.evaluate(
             ImmutableList.of(ModuleFileValue.KEY_FOR_ROOT_MODULE), evaluationContext);
     assertThat(result.hasError()).isTrue();
-    assertContainsEvent("The repo name 'foo' is already being used");
+    assertContainsEvent("The repo name 'foo' cannot be defined");
+    assertContainsEvent("as it is already defined");
   }
 
   @Test
@@ -1144,8 +1145,8 @@ public void testModuleExtensions_repoNameCollision_localRepoName() throws Except
     reporter.removeHandler(failFastHandler); // expect failures
     evaluator.evaluate(ImmutableList.of(skyKey), evaluationContext);
 
-    assertContainsEvent(
-        "The repo name 'mymod' is already being used as the current module name at");
+    assertContainsEvent("The repo name 'mymod' cannot be defined");
+    assertContainsEvent("as it is already defined as the current module name");
   }
 
   @Test
@@ -1491,7 +1492,8 @@ public void moduleRepoName_conflict() throws Exception {
     reporter.removeHandler(failFastHandler); // expect failures
     evaluator.evaluate(ImmutableList.of(ModuleFileValue.KEY_FOR_ROOT_MODULE), evaluationContext);
 
-    assertContainsEvent("The repo name 'bbb' is already being used as the module's own repo name");
+    assertContainsEvent("The repo name 'bbb' cannot be defined");
+    assertContainsEvent("as it is already defined as the module's own repo name");
   }
 
   @Test
diff --git a/src/test/py/bazel/bzlmod/bazel_overrides_test.py b/src/test/py/bazel/bzlmod/bazel_overrides_test.py
index 3fd7bd18a503d1..1cd1f064ddb160 100644
--- a/src/test/py/bazel/bzlmod/bazel_overrides_test.py
+++ b/src/test/py/bazel/bzlmod/bazel_overrides_test.py
@@ -720,11 +720,61 @@ def testInjectRepositoryOnExistingRepo(self):
         allow_failure=True,
     )
     self.AssertNotExitCode(exit_code, 0, stderr)
+    stderr = "\n".join(stderr)
     self.assertIn(
-        "Error in use_repo: The repo name 'my_repo' is already being used by"
-        ' --inject_repository at <builtin>',
+        "ERROR: The repo name 'my_repo' cannot be defined by"
+        ' --inject_repository at <builtin> as it is already defined by'
+        ' a use_repo() call at',
         stderr,
     )
+    self.assertIn(
+        'MODULE.bazel:2:9',
+        stderr,
+    )
+
+  def testInjectRepositoryRepoNameSideEffects(self):
+    self.ScratchFile(
+        'MODULE.bazel',
+        [
+            'local_repository = use_repo_rule("@//:defs.bzl", "local_repository")',
+            f'local_repository(name = "repo")',
+        ],
+    )
+    self.ScratchFile(
+        'defs.bzl',
+        [
+            'def _impl(ctx):',
+            '  ctx.file("BUILD")',
+            # Deliberate collision with `@bazel_tools//tools/build_defs/repo:local.bzl%local_repository`
+            'local_repository = repository_rule(implementation=_impl)',
+        ],
+    )
+    self.ScratchFile('BUILD')
+
+    self.ScratchFile('other_module/REPO.bazel')
+    self.ScratchFile('other_repo/BUILD', ['filegroup(name="target")'])
+
+    _, stdout, _ = self.RunBazel(['mod', 'dump_repo_mapping', ''])
+    self.assertIn(
+      '"+local_repository+repo"',
+      "\n".join(stdout),
+    )
+
+    # --inject_repository _must not_ affect `use_repo_rule` generated repo names.
+    _, stdout, _ = self.RunBazel([
+        'mod',
+        'dump_repo_mapping',
+        '',
+        '--inject_repository=injected_repo=%workspace%/other_repo',
+    ])
+    self.assertIn(
+      '"+local_repository+repo"',
+      "\n".join(stdout),
+    )
+    self.assertIn(
+      '"+local_repository2+injected_repo"',
+      "\n".join(stdout),
+    )
 
   def testOverrideRepositoryOnNonExistentRepo(self):
     self.ScratchFile('other_repo/REPO.bazel')