diff --git a/e2e/cli/test_hook_not_found_auto_install b/e2e/cli/test_hook_not_found_auto_install
new file mode 100755
index 0000000000..0505ed7e36
--- /dev/null
+++ b/e2e/cli/test_hook_not_found_auto_install
@@ -0,0 +1,51 @@
+#!/usr/bin/env bash
+
+# Test that not_found_auto_install works when a tool is already configured but not installed
+# Reproduces https://github.com/jdx/mise/discussions/6482#discussioncomment-14552091
+
+# Test 1: hook-not-found auto-install
+# Set up: Install tiny@3.1.0 globally
+mise use -g tiny@3.1.0
+assert "mise current tiny" "3.1.0"
+
+# Create a project that requires a different version (tiny@3.0.0)
+cat >mise.toml <<EOF
+[tools]
+tiny = "3.0.0"
+EOF
+
+# Uninstall the required version to simulate it being missing
+mise uninstall tiny@3.0.0 || true
+
+# Verify it's not installed
+assert_fail "mise ls tiny --installed | grep 3.0.0"
+
+# Simulate the hook-not-found behavior: rtx-tiny is requested but not installed
+# This should auto-install tiny@3.0.0 (note: tiny plugin provides rtx-tiny binary)
+mise hook-not-found rtx-tiny && mise current tiny | grep -q "3.0.0"
+assert_contains "mise ls tiny --installed" "3.0.0"
+
+# Clean up for next test
+rm -f mise.toml
+mise uninstall tiny@3.0.0
+
+# Test 2: shim auto-install
+# Set up: Install tiny@3.1.0 globally, configure tiny@3.0.0 locally (not installed)
+cat >mise.toml <<EOF
+[tools]
+tiny = "3.0.0"
+EOF
+
+# Verify it's not installed
+assert_fail "mise ls tiny --installed | grep 3.0.0"
+
+# Add shims to PATH and run the shimmed binary
+# This should auto-install tiny@3.0.0 via the shim
+export PATH="$MISE_DATA_DIR/shims:$PATH"
+rtx-tiny && mise current tiny | grep -q "3.0.0"
+assert_contains "mise ls tiny --installed" "3.0.0"
+
+# Clean up
+rm -f mise.toml
+mise use -g --rm tiny
+mise uninstall tiny --all
diff --git a/src/shims.rs b/src/shims.rs
index 0d77caddcf..1727c903d1 100644
--- a/src/shims.rs
+++ b/src/shims.rs
@@ -60,7 +60,7 @@ async fn which_shim(config: &mut Arc<Config>, bin_name: &str) -> Result<PathBuf>
             return Ok(bin);
         }
     }
-    if Settings::get().not_found_auto_install && console::user_attended() {
+    if Settings::get().not_found_auto_install {
         for tv in ts
             .install_missing_bin(config, bin_name)
             .await?
diff --git a/src/toolset/mod.rs b/src/toolset/mod.rs
index 6c7e84169a..8c25d2f2fd 100644
--- a/src/toolset/mod.rs
+++ b/src/toolset/mod.rs
@@ -860,12 +860,43 @@ impl Toolset {
         config: &mut Arc<Config>,
         bin_name: &str,
     ) -> Result<Option<Vec<ToolVersion>>> {
+        // Strategy: Find backends that could provide this bin by checking:
+        // 1. Any currently installed versions that provide the bin
+        // 2. Any requested backends with installed versions (even if not current)
         let mut plugins = IndexSet::new();
+
+        // First check currently active installed versions
         for (p, tv) in self.list_current_installed_versions(config) {
             if let Ok(Some(_bin)) = p.which(config, &tv, bin_name).await {
                 plugins.insert(p);
             }
         }
+
+        // Also check backends that are requested but not currently active
+        // This handles the case where a user has tool@v1 globally and tool@v2 locally (not installed)
+        // When looking for a bin provided by the tool, we check if any installed version provides it
+        let all_installed = self.list_installed_versions(config).await?;
+        for (backend, _versions) in self.list_versions_by_plugin() {
+            // Skip if we already found this backend
+            if plugins.contains(&backend) {
+                continue;
+            }
+
+            // Check if this backend has ANY installed version that provides the bin
+            let backend_versions: Vec<_> = all_installed
+                .iter()
+                .filter(|(p, _)| p.ba() == backend.ba())
+                .collect();
+
+            for (_, tv) in backend_versions {
+                if let Ok(Some(_bin)) = backend.which(config, tv, bin_name).await {
+                    plugins.insert(backend.clone());
+                    break;
+                }
+            }
+        }
+
+        // Install missing versions for backends that provide this bin
         for plugin in plugins {
             let versions = self
                 .list_missing_versions(config)