diff --git a/crates/ty/tests/cli/uv_workspace.rs b/crates/ty/tests/cli/uv_workspace.rs
index b321e9213e223..74e55a7ffda73 100644
--- a/crates/ty/tests/cli/uv_workspace.rs
+++ b/crates/ty/tests/cli/uv_workspace.rs
@@ -142,6 +142,86 @@ fn explicit_file_path_disables_uv_workspace_discovery() -> anyhow::Result<()> {
     Ok(())
 }
 
+/// Scripts discovered under a selected directory are independent uv projects and must not be
+/// analyzed as part of that directory's workspace member.
+#[cfg(feature = "test-uv")]
+#[test]
+fn implicitly_discovered_scripts_are_not_checked() -> anyhow::Result<()> {
+    let case = workspace_case()?;
+    case.write_file(
+        "packages/member/script.py",
+        r#"
+        # /// script
+        # dependencies = []
+        # ///
+
+        value: int = "ignored-script"
+        "#,
+    )?;
+    case.write_file(
+        "packages/member/nested/script.py",
+        r#"
+        # /// script
+        # dependencies = []
+        # ///
+
+        value: int = "ignored-nested-script"
+        "#,
+    )?;
+
+    let mut command = command_with_uv(&case, None)?;
+    command
+        .current_dir(case.root().join("packages/member"))
+        .arg(".");
+
+    assert_cmd_snapshot!(command, @r#"
+    success: false
+    exit_code: 1
+    ----- stdout -----
+    member.py:1:14: error[invalid-assignment] Object of type `Literal["selected-member"]` is not assignable to `int`
+    Found 1 diagnostic
+
+    ----- stderr -----
+    "#);
+
+    Ok(())
+}
+
+/// Selecting a script itself explicitly opts into checking that script even in uv integration
+/// mode.
+#[cfg(feature = "test-uv")]
+#[test]
+fn explicitly_selected_script_is_checked() -> anyhow::Result<()> {
+    let case = workspace_case()?;
+    case.write_file(
+        "packages/member/script.py",
+        r#"
+        # /// script
+        # dependencies = []
+        # ///
+
+        value: int = "selected-script"
+        "#,
+    )?;
+
+    let mut command = command_with_uv(&case, None)?;
+    command
+        .current_dir(case.root().join("packages/member"))
+        .arg("script.py");
+
+    assert_cmd_snapshot!(command, @r#"
+    success: false
+    exit_code: 1
+    ----- stdout -----
+    script.py:6:14: error[invalid-assignment] Object of type `Literal["selected-script"]` is not assignable to `int`
+    Found 1 diagnostic
+
+    ----- stderr -----
+    "#);
+
+    Ok(())
+}
+
 /// An explicitly selected member inherits ty rule configuration from the uv workspace root.
 #[cfg(feature = "test-uv")]
 #[test]
diff --git a/crates/ty_project/src/metadata.rs b/crates/ty_project/src/metadata.rs
index b87c086ff403f..e6439cf14df43 100644
--- a/crates/ty_project/src/metadata.rs
+++ b/crates/ty_project/src/metadata.rs
@@ -24,7 +24,7 @@ mod configuration_file;
 pub mod options;
 pub mod pyproject;
 pub mod python_version;
-mod script;
+pub(crate) mod script;
 pub mod settings;
 mod uv;
 pub mod value;
diff --git a/crates/ty_project/src/walk.rs b/crates/ty_project/src/walk.rs
index 6efea29574048..cae68037d45d0 100644
--- a/crates/ty_project/src/walk.rs
+++ b/crates/ty_project/src/walk.rs
@@ -1,4 +1,5 @@
 use crate::glob::IncludeExcludeFilter;
+use crate::metadata::script::script_metadata;
 use crate::{Db, GlobFilterCheckMode, IncludeResult, Project};
 use ruff_db::diagnostic::{Diagnostic, DiagnosticId, Severity};
 use ruff_db::files::{File, system_path_to_file};
@@ -167,6 +168,7 @@ impl ProjectFilesWalker {
         };
 
         let filter = ProjectFilesFilter::from_project(db, project);
+        let skip_implicit_scripts = project.metadata(db).has_uv_workspace();
         let files = std::sync::Mutex::new(Vec::new());
         let diagnostics = std::sync::Mutex::new(Vec::new());
 
@@ -259,6 +261,18 @@ impl ProjectFilesWalker {
                             // If this returns `Err`, then the file was deleted between now and when the walk callback was called.
                             // We can ignore this.
                             if let Ok(file) = system_path_to_file(&*db, entry.path()) {
+                                if entry.depth() > 0
+                                    && skip_implicit_scripts
+                                    && script_metadata(&*db, file).is_some()
+                                {
+                                    tracing::debug!(
+                                        "Ignoring implicitly discovered PEP 723 script `{path}` \
+                                        while uv integration is enabled.",
+                                        path = entry.path()
+                                    );
+                                    return WalkState::Skip;
+                                }
+
                                 files.lock().unwrap().push(file);
                             }
                         }