Beyond diagonal reconfigurable intelligent surface (BD-RIS) is a new architecture for RIS where elements are interconnected to provide more wave manipulation flexibility than traditional single connected RIS, enhancing data rate and coverage. However, channel estimation for BD-RIS is challenging due to the more complex multiple-connection structure involving their scattering elements. To address this issue, this paper proposes a decoupled channel estimation method for BD-RIS that yields separate estimates of the involved channels to enhance the accuracy of the overall combined channel by capitalizing on its Kronecker structure. Starting from a least squares estimate of the combined channel and by properly reshaping the resulting filtered signal, the proposed algorithm resorts to a Khatri-Rao Factorization (KRF) method that teases out the individual channels based on simple rank-one matrix approximation steps. Numerical results show that the proposed decoupled channel estimation yields more accurate channel estimates than the classical least squares scheme.