Why does my per-instance material color get wiped on prefab apply?

You modified material directly in scene; Apply All on the prefab pushes the prefab's material back. Use MaterialPropertyBlock for per-instance changes — it doesn't touch the shared material.

What's MaterialPropertyBlock?

Per-renderer override of shader properties without instantiating a new material. Cheap, GPU-instancing-friendly. Use SetPropertyBlock on the renderer.

For shared edits intentionally?

Edit the material asset directly in Project window; all instances pick up. Don't edit material from a scene reference unless you intend everyone to change.

Fix: Material Property Reset By Prefab Apply

Quick answer: Use MaterialPropertyBlock for per-instance shader properties. Avoids the shared-material trap.

Color tinted per enemy in scene. Designer applies the prefab. All tints revert.

The Fix

public class EnemyTint : MonoBehaviour {
    static readonly int ColorID = Shader.PropertyToID("_BaseColor");
    MaterialPropertyBlock _mpb;
    Renderer _r;

    void Start() {
        _r = GetComponent<Renderer>();
        _mpb = new MaterialPropertyBlock();
    }

    public void SetTint(Color c) {
        _r.GetPropertyBlock(_mpb);
        _mpb.SetColor(ColorID, c);
        _r.SetPropertyBlock(_mpb);
    }
}

MPB lives on the renderer instance. No shared material modification, no prefab desync.

Verifying

Set tint per enemy. Apply prefab: tints persist (they're on the renderer, not the material). Restart play: SetTint reapplies on Start.

“MPB per renderer. Prefab safe.”

Related Issues

For Shader Graph SubGraph, see SubGraph property. For keyword toggle, see keyword toggle.

MPB. Per instance. Safe.