diff --git a/src/bazel.rs b/src/bazel.rs
index 3877f0ae..6f57ad86 100644
--- a/src/bazel.rs
+++ b/src/bazel.rs
@@ -149,15 +149,29 @@ impl BazelOptions {
         &self,
         mut transform: impl FnMut(&mut Target),
     ) -> Result<Vec<Target>> {
-        let bzlmod_repos = if self.is_bzlmod_enabled()
-            && self.version().is_ok_and(|version| {
-                version >= BazelVersion(8, 6, 0) && version != BazelVersion(9, 0, 0)
-            }) {
-            self.query_bzlmod_repos(&mut transform)
-                .unwrap_or_else(|error| {
-                    eprintln!("[Warn] failed to hash Bzlmod repositories: {error:#}");
-                    Vec::new()
-                })
+        let bzlmod_repos = if self.is_bzlmod_enabled() {
+            let supports_bzlmod = match self.version() {
+                Ok(version) => version >= BazelVersion(8, 6, 0) && version != BazelVersion(9, 0, 0),
+                Err(error) if self.keep_going => {
+                    eprintln!(
+                        "[Warn] failed to check Bazel version for Bzlmod repositories: {error:#}"
+                    );
+                    false
+                }
+                Err(error) => return Err(error),
+            };
+            if supports_bzlmod {
+                match self.query_bzlmod_repos(&mut transform) {
+                    Ok(repos) => repos,
+                    Err(error) if self.keep_going => {
+                        eprintln!("[Warn] failed to hash Bzlmod repositories: {error:#}");
+                        Vec::new()
+                    }
+                    Err(error) => return Err(error),
+                }
+            } else {
+                Vec::new()
+            }
         } else {
             Vec::new()
         };
@@ -260,11 +274,11 @@ impl BazelOptions {
             bail!("bazel mod show_repo failed with {}", output.status);
         }
         let repositories = decode_delimited::<Repository>(output_file.path())?;
-        let module_edges = self
-            .module_graph_json()
-            .as_deref()
-            .map(parse_module_dependency_edges)
-            .unwrap_or_default();
+        let module_edges = match self.module_graph_json() {
+            Some(json) => parse_module_dependency_edges(&json),
+            None if self.keep_going => BTreeMap::new(),
+            None => bail!("bazel mod graph --output=json failed"),
+        };
         Ok(lower_repositories(
             repositories,
             &canonical_to_apparent,
@@ -1614,4 +1628,80 @@ exit 1
             .all(|character| character.is_ascii_hexdigit()));
         assert!(selected_repos_marker.is_file());
     }
+
+    #[test]
+    #[cfg(unix)]
+    fn query_bzlmod_repos_honors_keep_going() {
+        let workspace = tempfile::tempdir().unwrap();
+        let query_proto = workspace.path().join("query-result.pb");
+        write_delimited(&query_proto, &[rule_target("//app:lib")]);
+
+        // Fake Bazel where `mod graph` succeeds (`is_bzlmod_enabled()` is true),
+        // `version` returns 8.6.1, `mod dump_repo_mapping` returns an external repo,
+        // `mod show_repo` fails, and `query` writes `//app:lib` to `--output_file`.
+        let show_repo_fail_script = workspace.path().join("fake-bazel-show-repo-fail.sh");
+        let body = format!(
+            r#"#!/bin/sh
+args="$*"
+if echo "$args" | grep -q "mod graph"; then
+  echo "root"
+  exit 0
+fi
+if echo "$args" | grep -q "version"; then
+  echo "Build label: 8.6.1"
+  exit 0
+fi
+if echo "$args" | grep -q "mod dump_repo_mapping"; then
+  echo '{{"pip":"rules_python+0.31.0"}}'
+  exit 0
+fi
+if echo "$args" | grep -q "mod show_repo"; then
+  echo "transient fetch failure" >&2
+  exit 2
+fi
+while [ "$#" -gt 0 ]; do
+  if [ "$1" = "--output_file" ]; then
+    cp "{}" "$2"
+    exit 0
+  fi
+  shift
+done
+exit 1
+"#,
+            query_proto.display(),
+        );
+        fs::write(&show_repo_fail_script, body).unwrap();
+        let mut permissions = fs::metadata(&show_repo_fail_script).unwrap().permissions();
+        permissions.set_mode(0o755);
+        fs::set_permissions(&show_repo_fail_script, permissions).unwrap();
+
+        let mut options = BazelOptions {
+            workspace: workspace.path().to_path_buf(),
+            bazel: show_repo_fail_script,
+            startup_options: Vec::new(),
+            command_options: Vec::new(),
+            cquery_options: Vec::new(),
+            use_cquery: false,
+            cquery_expression: None,
+            keep_going: false,
+            fine_grained_external_repos: BTreeSet::new(),
+            exclude_external_targets: true,
+            exclude_targets_query: None,
+            no_bazelrc: false,
+            verbose: false,
+        };
+
+        let show_repo_err = options.query_all_targets().unwrap_err();
+        assert!(show_repo_err
+            .to_string()
+            .contains("bazel mod show_repo failed"));
+
+        // With `keep_going = true`, `query_all_targets` logs a warning and falls back to main targets.
+        options.keep_going = true;
+        let targets = options.query_all_targets().unwrap();
+        assert_eq!(
+            targets.iter().filter_map(target_name).collect::<Vec<_>>(),
+            ["//app:lib"]
+        );
+    }
 }