Architected materials can actively respond to external stimuli—such as mechanical forces, hydration and magnetic fields—by changing their geometries and thereby achieve novel functionalities. Such transformations are usually binary and volatile because they toggle between ‘on’ and ‘off’ states and require persistent external stimuli. Here we develop three-dimensional silicon-coated tetragonal microlattices that transform into sinusoidal patterns via cooperative beam buckling in response to an electrochemically driven silicon-lithium alloying reaction. In situ microscopy reveals a controllable, non-volatile and reversible structural transformation that forms multiple ordered buckling domains separated by distorted domain boundaries. We investigate the mechanical dynamics of individual buckling beams, cooperative coupling among neighbouring beams, and lithiation-rate-dependent distributions of domain sizes through chemo-mechanical modelling and statistical mechanics analysis. Our results highlight the critical role of defects and energy fluctuations in the dynamic response of architected materials. We further demonstrate that domain boundaries can be programmed to form particular patterns by pre-designing artificial defects, and that a variety of reconfigurational degrees of freedom can be achieved through micro-architecture design. This framework enables the design, fabrication, modelling, behaviour prediction and programming of electrochemically reconfigurable architected materials, and could open the way to beyond-intercalation battery electrodes, tunable phononic crystals and bio-implantable devices.