diff --git a/crates/uv-static/src/env_vars.rs b/crates/uv-static/src/env_vars.rs
index 1d054c6f6e803..3948eda7bce15 100644
--- a/crates/uv-static/src/env_vars.rs
+++ b/crates/uv-static/src/env_vars.rs
@@ -568,6 +568,12 @@ impl EnvVars {
     #[attr_added_in("0.9.15")]
     pub const UV_INTERNAL__TEST_LFS_DISABLED: &'static str = "UV_INTERNAL__TEST_LFS_DISABLED";
 
+    /// Marker variable to track whether `PYTHONHOME` was set by uv.
+    /// Used by the Windows trampoline to distinguish uv-set values from user-set values.
+    #[attr_hidden]
+    #[attr_added_in("next release")]
+    pub const UV_INTERNAL__PYTHONHOME: &'static str = "UV_INTERNAL__PYTHONHOME";
+
     /// Path to system-level configuration directory on Unix systems.
     #[attr_added_in("0.4.26")]
     pub const XDG_CONFIG_DIRS: &'static str = "XDG_CONFIG_DIRS";
diff --git a/crates/uv-trampoline-builder/trampolines/uv-trampoline-aarch64-console.exe b/crates/uv-trampoline-builder/trampolines/uv-trampoline-aarch64-console.exe
index 804e68d80c278..7e33bbaa7b223 100755
Binary files a/crates/uv-trampoline-builder/trampolines/uv-trampoline-aarch64-console.exe and b/crates/uv-trampoline-builder/trampolines/uv-trampoline-aarch64-console.exe differ
diff --git a/crates/uv-trampoline-builder/trampolines/uv-trampoline-aarch64-gui.exe b/crates/uv-trampoline-builder/trampolines/uv-trampoline-aarch64-gui.exe
index 7dbaa80a0dbf7..5355e550feed9 100755
Binary files a/crates/uv-trampoline-builder/trampolines/uv-trampoline-aarch64-gui.exe and b/crates/uv-trampoline-builder/trampolines/uv-trampoline-aarch64-gui.exe differ
diff --git a/crates/uv-trampoline-builder/trampolines/uv-trampoline-i686-console.exe b/crates/uv-trampoline-builder/trampolines/uv-trampoline-i686-console.exe
index 33f21a2b934e6..76317ecee6fb9 100755
Binary files a/crates/uv-trampoline-builder/trampolines/uv-trampoline-i686-console.exe and b/crates/uv-trampoline-builder/trampolines/uv-trampoline-i686-console.exe differ
diff --git a/crates/uv-trampoline-builder/trampolines/uv-trampoline-i686-gui.exe b/crates/uv-trampoline-builder/trampolines/uv-trampoline-i686-gui.exe
index 1e753c1fb4f95..23dab4f25c356 100755
Binary files a/crates/uv-trampoline-builder/trampolines/uv-trampoline-i686-gui.exe and b/crates/uv-trampoline-builder/trampolines/uv-trampoline-i686-gui.exe differ
diff --git a/crates/uv-trampoline-builder/trampolines/uv-trampoline-x86_64-console.exe b/crates/uv-trampoline-builder/trampolines/uv-trampoline-x86_64-console.exe
index a5a5ab6025785..36542006d7355 100755
Binary files a/crates/uv-trampoline-builder/trampolines/uv-trampoline-x86_64-console.exe and b/crates/uv-trampoline-builder/trampolines/uv-trampoline-x86_64-console.exe differ
diff --git a/crates/uv-trampoline-builder/trampolines/uv-trampoline-x86_64-gui.exe b/crates/uv-trampoline-builder/trampolines/uv-trampoline-x86_64-gui.exe
index 700fd94a649a3..0e8967ef6c127 100755
Binary files a/crates/uv-trampoline-builder/trampolines/uv-trampoline-x86_64-gui.exe and b/crates/uv-trampoline-builder/trampolines/uv-trampoline-x86_64-gui.exe differ
diff --git a/crates/uv-trampoline/src/bounce.rs b/crates/uv-trampoline/src/bounce.rs
index 761f5e4805565..d2cfb5fc01fd2 100644
--- a/crates/uv-trampoline/src/bounce.rs
+++ b/crates/uv-trampoline/src/bounce.rs
@@ -146,20 +146,35 @@ fn make_child_cmdline() -> CString {
                 // be correctly detected when using trampolines.
                 std::env::set_var(EnvVars::PYVENV_LAUNCHER, &executable_name);
 
-                // If this is not a virtual environment and `PYTHONHOME` has
-                // not been set, then set `PYTHONHOME` to the parent directory of
-                // the executable. This ensures that the correct installation
-                // directories are added to `sys.path` when running with a junction
-                // trampoline.
-                let python_home_set =
-                    std::env::var(EnvVars::PYTHONHOME).is_ok_and(|home| !home.is_empty());
-                if !is_virtualenv(python_exe.as_path()) && !python_home_set {
-                    std::env::set_var(
-                        EnvVars::PYTHONHOME,
-                        python_exe
+                // If this is not a virtual environment, set `PYTHONHOME` to
+                // the parent directory of the executable. This ensures that
+                // the correct installation directories are added to `sys.path`
+                // when running with a junction trampoline.
+                //
+                // We use a marker variable (`UV_INTERNAL__PYTHONHOME`) to track
+                // whether `PYTHONHOME` was set by uv. This allows us to:
+                // - Override inherited `PYTHONHOME` from parent Python processes
+                // - Preserve user-defined `PYTHONHOME` values
+                if !is_virtualenv(python_exe.as_path()) {
+                    let python_home = std::env::var(EnvVars::PYTHONHOME).ok();
+                    let marker = std::env::var(EnvVars::UV_INTERNAL__PYTHONHOME).ok();
+
+                    // Only set `PYTHONHOME` if:
+                    // - It's not set, OR
+                    // - It was set by uv (marker matches current `PYTHONHOME`)
+                    let should_override = match (&python_home, &marker) {
+                        (None, _) => true,
+                        (Some(home), Some(m)) if home == m => true,
+                        _ => false,
+                    };
+
+                    if should_override {
+                        let home = python_exe
                             .parent()
-                            .expect("Python executable should have a parent directory"),
-                    );
+                            .expect("Python executable should have a parent directory");
+                        std::env::set_var(EnvVars::PYTHONHOME, home);
+                        std::env::set_var(EnvVars::UV_INTERNAL__PYTHONHOME, home);
+                    }
                 }
             }
         }