The energy density of Li-ion batteries can be increased if graphitic anodes are replaced with nanostructured Si-based materials. Design of efficient Si anodes requires a better fundamental understanding of the possible changes in Si-Li alloy morphology during cycling. Here we propose a simple elastoplastic model to predict morphological changes in Si upon electrochemical reaction with Li in a confined geometry, such as a pore of a carbon nanotube (CNT). Our experiments with CNTs having inner Si coatings of different thicknesses confirmed the theoretical predictions and demonstrated irreversible shape changes in the first cycle and fully reversible shape changes in subsequent cycles. During the first lithiation, Si was found to adapt to the restricted shape of the rigid CNT pore and plastically deform during electrochemical alloying with Li. The sequential Li insertion and extraction periodically alters the tube size between the expanded and contracted states. The produced samples of porous Si with rigid CNT outer shell showed capacity up to 2100 mAh/g, stable performance for over 250 cycles, and outstanding average Coulombic efficiency in excess of 99.9%. CNT walls were demonstrated to withstand stresses caused by the initial Si expansion and Li intercalation.