diff --git a/compiler/rustc_metadata/src/creader.rs b/compiler/rustc_metadata/src/creader.rs
index 44a3e9760e1e1..2c27c75229086 100644
--- a/compiler/rustc_metadata/src/creader.rs
+++ b/compiler/rustc_metadata/src/creader.rs
@@ -235,7 +235,9 @@ impl CStore {
     pub(crate) fn crate_dependencies_in_postorder(&self, cnum: CrateNum) -> Vec<CrateNum> {
         let mut deps = Vec::new();
         if cnum == LOCAL_CRATE {
-            for (cnum, _) in self.iter_crate_data() {
+            for cnum in
+                self.iter_crate_data().filter_map(|(cnum, data)| data.used().then_some(cnum))
+            {
                 self.push_dependencies_in_postorder(&mut deps, cnum);
             }
         } else {
diff --git a/tests/run-make/issue-125484-used-dependencies/dependency.rs b/tests/run-make/issue-125484-used-dependencies/dependency.rs
new file mode 100644
index 0000000000000..d15abba59766b
--- /dev/null
+++ b/tests/run-make/issue-125484-used-dependencies/dependency.rs
@@ -0,0 +1 @@
+// Empty
diff --git a/tests/run-make/issue-125484-used-dependencies/main.rs b/tests/run-make/issue-125484-used-dependencies/main.rs
new file mode 100644
index 0000000000000..0c1a1f8208ad0
--- /dev/null
+++ b/tests/run-make/issue-125484-used-dependencies/main.rs
@@ -0,0 +1,9 @@
+pub type Foo = something::same::Thing;
+
+mod something {
+    pub mod same {
+        pub struct Thing;
+    }
+}
+
+fn main() {}
diff --git a/tests/run-make/issue-125484-used-dependencies/rmake.rs b/tests/run-make/issue-125484-used-dependencies/rmake.rs
new file mode 100644
index 0000000000000..b75e82b42db7b
--- /dev/null
+++ b/tests/run-make/issue-125484-used-dependencies/rmake.rs
@@ -0,0 +1,18 @@
+// Non-regression test for issues #125474, #125484, #125646, with the repro taken from #125484. Some
+// queries use "used dependencies" while others use "speculatively loaded dependencies", and an
+// indexing ICE appeared in some cases when these were unexpectedly used in the same context.
+
+// FIXME: this should probably be a UI test instead of a run-make test, but I *cannot* find a way to
+// make compiletest annotations reproduce the ICE with the minimizations from issues #125474 and
+// #125484.
+
+use run_make_support::{rustc, tmp_dir};
+
+fn main() {
+    // The dependency is not itself significant, apart from sharing a name with one of main's
+    // modules.
+    rustc().crate_name("same").crate_type("rlib").input("dependency.rs").run();
+
+    // Here, an ICE would happen when building the linker command.
+    rustc().input("main.rs").extern_("same", tmp_dir().join("libsame.rlib")).run();
+}