diff --git a/e2e/cli/test_test_tool_clean b/e2e/cli/test_test_tool_clean
new file mode 100755
index 0000000000..729e39d5e9
--- /dev/null
+++ b/e2e/cli/test_test_tool_clean
@@ -0,0 +1,52 @@
+#!/usr/bin/env bash
+
+set -euxo pipefail
+
+# Test 1: Verify test-tool cleans existing installations before running
+echo "=== Test 1: Clean existing installations ==="
+
+# Install multiple versions first
+mise install shellcheck@0.9.0
+mise install shellcheck@0.10.0
+
+# Verify both versions are installed
+mise ls shellcheck | grep "0.9.0"
+mise ls shellcheck | grep "0.10.0"
+[ -d "$MISE_DATA_DIR/installs/shellcheck/0.9.0" ]
+[ -d "$MISE_DATA_DIR/installs/shellcheck/0.10.0" ]
+
+# Create a marker file to verify directories are cleaned
+touch "$MISE_DATA_DIR/installs/shellcheck/marker.txt"
+touch "$MISE_CACHE_DIR/shellcheck/marker.txt" 2>/dev/null || true
+
+# Run test-tool which should clean everything first and succeed
+mise test-tool shellcheck
+
+# Verify the marker files are gone (directories were cleaned)
+if [ -f "$MISE_DATA_DIR/installs/shellcheck/marker.txt" ]; then
+	echo "ERROR: installs directory was not cleaned"
+	exit 1
+fi
+
+# Verify test-tool installed the latest version
+mise ls shellcheck | grep -E "0\.[0-9]+\.[0-9]+"
+[ -d "$MISE_DATA_DIR/installs/shellcheck" ]
+
+# Test 2: Verify cache directory is cleaned
+echo "=== Test 2: Cache directory cleaning ==="
+
+# Create cache content
+mkdir -p "$MISE_CACHE_DIR/shellcheck"
+echo "cached data" >"$MISE_CACHE_DIR/shellcheck/test.cache"
+
+# Run test-tool again
+mise test-tool shellcheck
+
+# Verify cache was cleaned and recreated
+[ -d "$MISE_CACHE_DIR/shellcheck" ]
+if [ -f "$MISE_CACHE_DIR/shellcheck/test.cache" ]; then
+	echo "ERROR: cache directory was not cleaned"
+	exit 1
+fi
+
+echo "Test passed: test-tool correctly cleans all directories before installing"
diff --git a/src/cli/test_tool.rs b/src/cli/test_tool.rs
index 3b22ff576e..7dd2ff5d4f 100644
--- a/src/cli/test_tool.rs
+++ b/src/cli/test_tool.rs
@@ -148,6 +148,46 @@ impl TestTool {
         cmd: &str,
         expected: &str,
     ) -> Result<()> {
+        // First, clean all backend data by removing directories
+        let pr = crate::ui::multi_progress_report::MultiProgressReport::get()
+            .add(&format!("cleaning {}", tool.short));
+
+        let mut cleaned_any = false;
+
+        // Remove entire installs directory for this tool
+        if tool.ba.installs_path.exists() {
+            info!(
+                "Removing installs directory: {}",
+                tool.ba.installs_path.display()
+            );
+            file::remove_all(&tool.ba.installs_path)?;
+            cleaned_any = true;
+        }
+
+        // Clear cache directory (contains metadata)
+        if tool.ba.cache_path.exists() {
+            info!("Removing cache directory: {}", tool.ba.cache_path.display());
+            file::remove_all(&tool.ba.cache_path)?;
+            cleaned_any = true;
+        }
+
+        // Clear downloads directory
+        if tool.ba.downloads_path.exists() {
+            info!(
+                "Removing downloads directory: {}",
+                tool.ba.downloads_path.display()
+            );
+            file::remove_all(&tool.ba.downloads_path)?;
+            cleaned_any = true;
+        }
+
+        pr.finish();
+
+        // Reset the config to clear in-memory backend metadata caches if we cleaned anything
+        if cleaned_any {
+            *config = Config::reset().await?;
+        }
+
         let mut args = vec![tool.clone()];
         args.extend(
             tool.ba