diff --git a/tools/rust_analyzer/aquery.rs b/tools/rust_analyzer/aquery.rs
index 83f8ac2922..6fc9c2ff3c 100644
--- a/tools/rust_analyzer/aquery.rs
+++ b/tools/rust_analyzer/aquery.rs
@@ -94,7 +94,22 @@ pub fn get_crate_specs(
 ) -> anyhow::Result<BTreeSet<CrateSpec>> {
     log::info!("running bazel aquery...");
     log::debug!("Get crate specs with targets: {:?}", targets);
-    let target_pattern = format!("deps({})", targets.join("+"));
+    let target_pattern = format!(
+        "deps({})",
+        targets
+            .iter()
+            .map(|t| {
+                if let Some(stripped) = t.strip_prefix('-') {
+                    format!(" - {stripped}")
+                } else {
+                    format!(" + {t}")
+                }
+            })
+            .collect::<Vec<_>>()
+            .join("")
+            .trim_start_matches(" + ")
+            .to_owned()
+    );
 
     let mut aquery_command = bazel_command(bazel, Some(workspace), Some(output_base));
     aquery_command
diff --git a/tools/rust_analyzer/lib.rs b/tools/rust_analyzer/lib.rs
index 4ea641e6a0..dcc5ecf0f4 100644
--- a/tools/rust_analyzer/lib.rs
+++ b/tools/rust_analyzer/lib.rs
@@ -112,6 +112,7 @@ fn generate_crate_info(
             "--aspects={rules_rust}//rust:defs.bzl%rust_analyzer_aspect"
         ))
         .arg("--output_groups=rust_analyzer_crate_spec,rust_generated_srcs,rust_analyzer_proc_macro_dylib,rust_analyzer_src")
+        .arg("--")
         .args(targets)
         .output()?;