The D3-D5 probe-brane system is holographically dual to a defect CFT which is known to be integrable. The evidence comes mainly from the study of correlation functions at weak coupling. In the present work we shed light on the emergence of integrability on the string theory side. We do so by constructing the double row transfer matrix which is conserved when the appropriate boundary conditions are imposed. The corresponding reflection matrix turns out to be dynamical and depends both on the spectral parameter and the string embedding coordinates.