Core shell structures are of prime importance for applications in chemistry, optics and magnetism. Even though core shell structures can be currently prepared by the chemical route, the stability is questioned when particles are as deposited or embedded in a matrix. We show that the core shell structure of the CoAg clusters is definitively destroyed when they are embedded in a silicon matrix. A careful inspection of the phase diagram is essential to predict the core shell structure conservation. Transmission Electronic Microscopy (TEM) and X-ray Photoemission Spectroscopy (XPS) are used to clear up the matrix effect. (C) 2013 Elsevier B. V. All rights reserved.