diff --git a/src/bazel.rs b/src/bazel.rs
index 07026a89..7b01c534 100644
--- a/src/bazel.rs
+++ b/src/bazel.rs
@@ -1532,7 +1532,9 @@ impl BazelOptions {
         };
         if let Some(compatible) = compatible {
             targets.retain(|target| {
-                target_name(target).is_some_and(|name| compatible.contains(target_label(name)))
+                target_name(target).is_some_and(|name| {
+                    compatible.contains(main_repo_label_key(target_label(name)))
+                })
             });
         }
         Ok(targets)
@@ -1552,12 +1554,10 @@ impl BazelOptions {
         if "<alias target" in target_repr:
             # repr() prints a main-repository alias with its apparent label
             # (`//:tool`) even under --consistent_labels, while every other
-            # target is canonical (`@@//:tool`). Normalize so the alias
-            # matches the label it is later looked up by.
-            label = target_repr.split(" ")[2]
-            if label.startswith("//"):
-                label = "@@" + label
-            return label
+            # target comes back as `@@//:tool` under Bzlmod and `@//:tool` in
+            # WORKSPACE mode. The labels are compared through
+            # main_repo_label_key, which puts all three in one form.
+            return target_repr.split(" ")[2]
         return str(target.label)
     return ""
 "#,
@@ -1586,7 +1586,7 @@ impl BazelOptions {
         Ok(String::from_utf8_lossy(&output.stdout)
             .lines()
             .filter(|line| !line.trim().is_empty())
-            .map(str::to_owned)
+            .map(|line| main_repo_label_key(line).to_owned())
             .collect())
     }
 
@@ -2937,6 +2937,18 @@ pub fn target_label(key: &str) -> &str {
     split_configured(key).0
 }
 
+/// One spelling of a main-repository label, for comparing labels Bazel printed in
+/// different forms: `@@//pkg:name` (Bzlmod), `@//pkg:name` (WORKSPACE mode) and the
+/// apparent `//pkg:name` that `repr()` gives a main-repository alias all become
+/// `//pkg:name`. Other labels are returned unchanged.
+fn main_repo_label_key(label: &str) -> &str {
+    label
+        .strip_prefix("@@")
+        .or_else(|| label.strip_prefix('@'))
+        .filter(|rest| rest.starts_with("//"))
+        .unwrap_or(label)
+}
+
 pub fn target_name(target: &Target) -> Option<&str> {
     match target.r#type {
         target::Discriminator::Rule => target.rule.as_option().map(|rule| rule.name.as_str()),
@@ -3797,6 +3809,19 @@ mod tests {
         );
     }
 
+    #[test]
+    fn main_repo_label_key_puts_main_repository_labels_in_one_form() {
+        // Bzlmod, WORKSPACE mode and repr() of a main-repository alias.
+        for label in ["@@//pkg:name", "@//pkg:name", "//pkg:name"] {
+            assert_eq!(main_repo_label_key(label), "//pkg:name", "{label}");
+        }
+        assert_eq!(main_repo_label_key("@@//:tool"), "//:tool");
+        // External repositories keep their name, in either spelling.
+        for label in ["@@rules_cc+//cc:defs", "@rules_cc//cc:defs", "@@foo//:bar"] {
+            assert_eq!(main_repo_label_key(label), label, "{label}");
+        }
+    }
+
     #[test]
     fn target_names_and_lowering_cover_all_target_types() {
         let source = Target {
diff --git a/tests/e2e/regressions.rs b/tests/e2e/regressions.rs
index dbe91f5f..42d4c2b4 100644
--- a/tests/e2e/regressions.rs
+++ b/tests/e2e/regressions.rs
@@ -1340,3 +1340,64 @@ fn main_repo_alias_change_reaches_consumer_cquery() {
         );
     }
 }
+
+/// Follow-up to <https://github.com/Tinder/bazel-diff/issues/612> for WORKSPACE mode: there
+/// `--consistent_labels` prints main-repository targets as `@//:tool`, not the Bzlmod
+/// `@@//:tool`, so prefixing the alias's apparent label with `@@` still left it unmatched,
+/// dropped as if it were platform-incompatible together with every edge through it.
+#[test]
+fn main_repo_alias_change_reaches_consumer_cquery_workspace_mode() {
+    let first = copy_workspace("cquery_main_repo_alias_workspace");
+    let second = copy_workspace("cquery_main_repo_alias_workspace");
+    fs::write(second.path().join("bar/baz.txt"), "after\n").unwrap();
+
+    let output = tempfile::tempdir().unwrap();
+    let from = output.path().join("from.json");
+    let to = output.path().join("to.json");
+    let edges_file = output.path().join("edges.json");
+    let result = output.path().join("impacted.txt");
+    assert!(generate(first.path(), &from, &["--useCquery"])
+        .status
+        .success());
+    assert!(generate(
+        second.path(),
+        &to,
+        &[
+            "--useCquery",
+            "--depEdgesFile",
+            edges_file.to_str().unwrap()
+        ],
+    )
+    .status
+    .success());
+    assert!(impacted(second.path(), &from, &to, &result, &[])
+        .status
+        .success());
+
+    let hashes = hashes(&to);
+    assert!(
+        hashes.keys().any(|label| label.ends_with("//:tool")),
+        "the alias //:tool was dropped from the cquery hashes: {:?}",
+        hashes.keys().collect::<Vec<_>>()
+    );
+    let edges = dep_edges(&edges_file);
+    let wrapper_edges = edges
+        .iter()
+        .find(|(label, _)| label.ends_with("//:wrapper"))
+        .map(|(_, deps)| deps.clone())
+        .expect("//:wrapper has dep edges");
+    assert!(
+        wrapper_edges.iter().any(|dep| dep.ends_with("//:tool")),
+        "//:wrapper lost its edge to the alias //:tool: {wrapper_edges:?}"
+    );
+
+    let impacted = read_lines(&result);
+    for name in ["//bar:baz.txt", "//bar:baz", "//:tool", "//:wrapper"] {
+        assert!(
+            impacted
+                .iter()
+                .any(|label| label == name || label.trim_start_matches('@') == name),
+            "{name} should be impacted through the alias under cquery, got {impacted:?}"
+        );
+    }
+}
diff --git a/tests/resources/workspaces/cquery_main_repo_alias_workspace/.bazelrc b/tests/resources/workspaces/cquery_main_repo_alias_workspace/.bazelrc
new file mode 100644
index 00000000..409363ea
--- /dev/null
+++ b/tests/resources/workspaces/cquery_main_repo_alias_workspace/.bazelrc
@@ -0,0 +1,4 @@
+# Main-repository labels print as `@//pkg:name` in WORKSPACE mode, unlike the
+# `@@//pkg:name` of Bzlmod; run this fixture in WORKSPACE mode.
+common --noenable_bzlmod
+common --enable_workspace
diff --git a/tests/resources/workspaces/cquery_main_repo_alias_workspace/BUILD.bazel b/tests/resources/workspaces/cquery_main_repo_alias_workspace/BUILD.bazel
new file mode 100644
index 00000000..a03cb29a
--- /dev/null
+++ b/tests/resources/workspaces/cquery_main_repo_alias_workspace/BUILD.bazel
@@ -0,0 +1,14 @@
+# A main-repository alias in front of the file that changes. `//:wrapper`
+# reaches `bar/baz.txt` only through the alias, so it must be impacted when
+# the file changes.
+alias(
+    name = "tool",
+    actual = "//bar:baz",
+)
+
+genrule(
+    name = "wrapper",
+    srcs = [":tool"],
+    outs = ["wrapper.txt"],
+    cmd = "cat $(SRCS) > $@",
+)
diff --git a/tests/resources/workspaces/cquery_main_repo_alias_workspace/README.md b/tests/resources/workspaces/cquery_main_repo_alias_workspace/README.md
new file mode 100644
index 00000000..d6ac6968
--- /dev/null
+++ b/tests/resources/workspaces/cquery_main_repo_alias_workspace/README.md
@@ -0,0 +1,23 @@
+# Main-repository alias under cquery, in WORKSPACE mode
+
+The WORKSPACE-mode counterpart of `cquery_main_repo_alias` (GitHub Issue #612).
+
+## The graph
+
+`//:wrapper` (a `genrule`) lists `//:tool` in its `srcs`. `//:tool` is an
+`alias` of `//bar:baz`, a `filegroup` over `bar/baz.txt`.
+
+## Expected behaviour
+
+Changing `bar/baz.txt` impacts `//bar:baz.txt`, `//bar:baz`, `//:tool`,
+`//:wrapper` and `//:wrapper.txt`, in query mode and in cquery mode alike.
+
+## Behaviour before the fix
+
+The compatible-target cquery names an alias by `repr(target)`, which prints a
+main-repository alias with its apparent label (`//:tool`). The fix for #612
+prefixed it with `@@`, the main repository's canonical form under Bzlmod. In
+WORKSPACE mode, though, `--consistent_labels` prints main-repository targets
+as `@//:tool`, so `@@//:tool` still never matches, the alias is dropped as if
+it were incompatible, and so is every edge from `//:wrapper` through it. Under
+cquery only `//bar:baz` and `//bar:baz.txt` are reported as impacted.
diff --git a/tests/resources/workspaces/cquery_main_repo_alias_workspace/WORKSPACE b/tests/resources/workspaces/cquery_main_repo_alias_workspace/WORKSPACE
new file mode 100644
index 00000000..43ba6189
--- /dev/null
+++ b/tests/resources/workspaces/cquery_main_repo_alias_workspace/WORKSPACE
@@ -0,0 +1 @@
+workspace(name = "cquery_main_repo_alias_workspace")
diff --git a/tests/resources/workspaces/cquery_main_repo_alias_workspace/bar/BUILD.bazel b/tests/resources/workspaces/cquery_main_repo_alias_workspace/bar/BUILD.bazel
new file mode 100644
index 00000000..e31cb197
--- /dev/null
+++ b/tests/resources/workspaces/cquery_main_repo_alias_workspace/bar/BUILD.bazel
@@ -0,0 +1,5 @@
+filegroup(
+    name = "baz",
+    srcs = ["baz.txt"],
+    visibility = ["//visibility:public"],
+)
diff --git a/tests/resources/workspaces/cquery_main_repo_alias_workspace/bar/baz.txt b/tests/resources/workspaces/cquery_main_repo_alias_workspace/bar/baz.txt
new file mode 100644
index 00000000..90be1f30
--- /dev/null
+++ b/tests/resources/workspaces/cquery_main_repo_alias_workspace/bar/baz.txt
@@ -0,0 +1 @@
+before
diff --git a/tools/e2e/rust_e2e_cases.bzl b/tools/e2e/rust_e2e_cases.bzl
index 921847cc..18967fe1 100644
--- a/tools/e2e/rust_e2e_cases.bzl
+++ b/tools/e2e/rust_e2e_cases.bzl
@@ -235,6 +235,10 @@ RUST_E2E_SUITES = [
                 "name": "regressions::main_repo_alias_change_reaches_consumer_cquery",
                 "timeout": "moderate",
             },
+            {
+                "name": "regressions::main_repo_alias_change_reaches_consumer_cquery_workspace_mode",
+                "timeout": "moderate",
+            },
             {
                 "name": "regressions::main_repo_alias_change_reaches_consumer_query",
                 "timeout": "moderate",