diff --git a/crates/pm/src/cmd/clean.rs b/crates/pm/src/cmd/clean.rs
index a10a645d8..e916a9cde 100644
--- a/crates/pm/src/cmd/clean.rs
+++ b/crates/pm/src/cmd/clean.rs
@@ -2,12 +2,11 @@ use anyhow::{Context, Result};
 use std::io::{self, Write};
 use tokio::fs;
 
-use crate::util::cache::{collect_matching_versions, matches_pattern, parse_pattern};
+use crate::util::cache::{collect_matching_versions, get_cache_dir, matches_pattern, parse_pattern};
 
 pub async fn clean(pattern: &str) -> Result<()> {
-    let cache_dir = dirs::home_dir()
-        .map(|p| p.join(".cache").join("nm"))
-        .context("Failed to get cache directory")?;
+    // Use get_cache_dir() which includes registry isolation
+    let cache_dir = get_cache_dir();
 
     let (pkg_pattern, version_pattern) = parse_pattern(pattern);
     let mut to_delete = Vec::new();
diff --git a/crates/pm/src/util/cache.rs b/crates/pm/src/util/cache.rs
index 178c6d22c..5b535ea35 100644
--- a/crates/pm/src/util/cache.rs
+++ b/crates/pm/src/util/cache.rs
@@ -84,8 +84,21 @@ pub async fn collect_matching_versions(
     Ok(())
 }
 
+/// Converts registry URL to directory name by removing protocol prefix and trailing slash.
+fn registry_to_dir_name(registry_url: &str) -> String {
+    let url = registry_url
+        .strip_prefix("https://")
+        .or_else(|| registry_url.strip_prefix("http://"))
+        .unwrap_or(registry_url);
+    url.trim_end_matches('/').to_string()
+}
+
+/// Returns cache directory path with registry isolation: ~/.cache/nm/registry-host/
 pub fn get_cache_dir() -> PathBuf {
-    config::get_cache_dir()
+    let base_cache_dir = config::get_cache_dir();
+    let registry = config::get_registry();
+    let registry_dir = registry_to_dir_name(&registry);
+    base_cache_dir.join(registry_dir)
 }
 
 pub fn get_package_versions_cache_file(package_name: &str) -> PathBuf {
@@ -265,6 +278,26 @@ mod tests {
         Ok(())
     }
 
+    #[test]
+    fn test_registry_to_dir_name() {
+        assert_eq!(
+            registry_to_dir_name("https://registry.npmjs.org"),
+            "registry.npmjs.org"
+        );
+        assert_eq!(
+            registry_to_dir_name("https://registry.npmmirror.com"),
+            "registry.npmmirror.com"
+        );
+        assert_eq!(
+            registry_to_dir_name("https://registry.npmjs.org/"),
+            "registry.npmjs.org"
+        );
+        assert_eq!(
+            registry_to_dir_name("http://registry.npmjs.org"),
+            "registry.npmjs.org"
+        );
+    }
+
     #[test]
     fn test_get_cache_dir_uses_config() {
         // Test that get_cache_dir delegates to config module
@@ -274,6 +307,17 @@ mod tests {
         assert!(result.is_absolute() || result.starts_with("~") || result.starts_with("."));
     }
 
+    #[test]
+    fn test_get_cache_dir_includes_registry() {
+        // Test that cache directory includes registry dimension
+        let cache_dir = get_cache_dir();
+        let cache_dir_str = cache_dir.to_string_lossy();
+        
+        // Should contain registry directory name
+        // The exact structure depends on current registry setting
+        assert!(cache_dir_str.contains("nm") || cache_dir_str.contains("cache"));
+    }
+
     #[test]
     fn test_get_package_versions_cache_file() {
         let result = get_package_versions_cache_file("lodash");