The morphological and chemical modifications induced by repeated cycling of conversion-type negative electrode material were studied for iron sulfide thin films in 1M-LiClO4/PC by combining AFM, XPS and ToF-SIMS analysis with electrochemical control. The topographical changes were consistent with irreversible swelling of the material caused by repeated volume expansion/contraction. A 3% capacity fading measured after 9 conversion/deconversion cycles resulted mainly from the loss of electroactive material forming pinhole defects in the thin film electrode. Repeated cycling caused increasing accumulation of non deconverted material in the bulk thin film electrode. Repeated cycling also resulted in continuous surface up-take and increasing accumulation of the SEI layer in the bulk thin film electrode, rich in Li2CO3. Formation of a duplex-like structure with organic and inorganic compounds primarily distributed in the outer and inner parts, respectively, was suggested by ToF-SIMS depth profiling of the SEI layer.