Due to large mixing in the stop sector, one up-type squark can become rather light. If the mass difference of the lightest up-type squark and the lightest neutralino is sufficiently small, both the decay of the lightest up-type squark into a top quark and the neutralino and the decay into a W boson, a bottom quark and the neutralino are kinematically suppressed. We present the calculation of the decay width of the lightest up-type squark in the MSSM with a general flavor structure in two different decay modes which are important in this regime: the flavor changing neutral current two-body decay into a charm- or an up-quark and the neutralino with SUSY-QCD NLO corrections and the four-body decay into three Standard Model fermions and the neutralino with masses of third generation fermions taken into account in the final states.