diff --git a/sqlx-cli/src/metadata.rs b/sqlx-cli/src/metadata.rs
index bb6afc6339..afcc79ac03 100644
--- a/sqlx-cli/src/metadata.rs
+++ b/sqlx-cli/src/metadata.rs
@@ -56,6 +56,9 @@ pub struct Metadata {
     ///
     /// Typically `target` at the workspace root, but can be overridden
     target_directory: PathBuf,
+    /// Package metadata for the crate in the current working directory, None if run from
+    /// a workspace with the `merged` flag.
+    current_package: Option<Package>,
 }
 
 impl Metadata {
@@ -75,6 +78,10 @@ impl Metadata {
         &self.target_directory
     }
 
+    pub fn current_package(&self) -> Option<&Package> {
+        self.current_package.as_ref()
+    }
+
     /// Gets all dependents (direct and transitive) of `id`
     pub fn all_dependents_of(&self, id: &MetadataId) -> BTreeSet<&MetadataId> {
         let mut dependents = BTreeSet::new();
@@ -101,13 +108,19 @@ impl FromStr for Metadata {
     type Err = anyhow::Error;
 
     fn from_str(s: &str) -> Result<Self, Self::Err> {
+        let cargo_metadata: CargoMetadata = serde_json::from_str(s)?;
+
+        // Extract the package for the current working directory, will be empty if running
+        // from a workspace root.
+        let current_package: Option<Package> = cargo_metadata.root_package().map(Package::from);
+
         let CargoMetadata {
             packages: metadata_packages,
             workspace_members,
             resolve,
             target_directory,
             ..
-        } = serde_json::from_str(s)?;
+        } = cargo_metadata;
 
         let mut packages = BTreeMap::new();
         for metadata_package in metadata_packages {
@@ -136,6 +149,7 @@ impl FromStr for Metadata {
             workspace_members,
             reverse_deps,
             target_directory,
+            current_package,
         })
     }
 }
diff --git a/sqlx-cli/src/prepare.rs b/sqlx-cli/src/prepare.rs
index 77d17c8ec3..2bcb4f4bff 100644
--- a/sqlx-cli/src/prepare.rs
+++ b/sqlx-cli/src/prepare.rs
@@ -180,7 +180,23 @@ hint: This command only works in the manifest directory of a Cargo package."#
         bail!("`cargo check` failed with status: {}", check_status);
     }
 
-    let pattern = metadata.target_directory().join("sqlx/query-*.json");
+    let package_dir = if merge {
+        // Merge queries from all workspace crates.
+        "**"
+    } else {
+        // Use a separate sub-directory for each crate in a workspace. This avoids a race condition
+        // where `prepare` can pull in queries from multiple crates if they happen to be generated
+        // simultaneously (e.g. Rust Analyzer building in the background).
+        metadata
+            .current_package()
+            .map(|pkg| pkg.name())
+            .context("Resolving the crate package for the current working directory failed")?
+    };
+    let pattern = metadata
+        .target_directory()
+        .join("sqlx")
+        .join(package_dir)
+        .join("query-*.json");
 
     let mut data = BTreeMap::new();
 
diff --git a/sqlx-cli/tests/assets/sample_metadata.json b/sqlx-cli/tests/assets/sample_metadata.json
index 7c57b276a2..74752d4a18 100644
--- a/sqlx-cli/tests/assets/sample_metadata.json
+++ b/sqlx-cli/tests/assets/sample_metadata.json
@@ -30506,7 +30506,7 @@
         "features": []
       }
     ],
-    "root": null
+    "root": "b_in_workspace_lib 0.1.0 (path+file:///home/user/problematic/workspace/b_in_workspace_lib)"
   },
   "target_directory": "/home/user/problematic/workspace/target",
   "version": 1,
diff --git a/sqlx-macros/src/query/mod.rs b/sqlx-macros/src/query/mod.rs
index e036fd72c9..44a540be8e 100644
--- a/sqlx-macros/src/query/mod.rs
+++ b/sqlx-macros/src/query/mod.rs
@@ -31,6 +31,8 @@ struct Metadata {
     offline: bool,
     database_url: Option<String>,
     #[cfg(feature = "offline")]
+    package_name: String,
+    #[cfg(feature = "offline")]
     target_dir: PathBuf,
     #[cfg(feature = "offline")]
     workspace_root: Arc<Mutex<Option<PathBuf>>>,
@@ -74,6 +76,11 @@ static METADATA: Lazy<Metadata> = Lazy::new(|| {
         .expect("`CARGO_MANIFEST_DIR` must be set")
         .into();
 
+    #[cfg(feature = "offline")]
+    let package_name: String = env("CARGO_PKG_NAME")
+        .expect("`CARGO_PKG_NAME` must be set")
+        .into();
+
     #[cfg(feature = "offline")]
     let target_dir = env("CARGO_TARGET_DIR").map_or_else(|_| "target".into(), |dir| dir.into());
 
@@ -110,6 +117,8 @@ static METADATA: Lazy<Metadata> = Lazy::new(|| {
         offline,
         database_url,
         #[cfg(feature = "offline")]
+        package_name,
+        #[cfg(feature = "offline")]
         target_dir,
         #[cfg(feature = "offline")]
         workspace_root: Arc::new(Mutex::new(None)),
@@ -402,7 +411,13 @@ where
     // If the build is offline, the cache is our input so it's pointless to also write data for it.
     #[cfg(feature = "offline")]
     if !offline {
-        let save_dir = METADATA.target_dir.join("sqlx");
+        // Use a separate sub-directory for each crate in a workspace. This avoids a race condition
+        // where `prepare` can pull in queries from multiple crates if they happen to be generated
+        // simultaneously (e.g. Rust Analyzer building in the background).
+        let save_dir = METADATA
+            .target_dir
+            .join("sqlx")
+            .join(&METADATA.package_name);
         std::fs::create_dir_all(&save_dir)?;
         data.save_in(save_dir, input.src_span)?;
     }