The present disclosure provides electroporation cartridges for single use electroporation as well as electroporation cartridges for automated batch processing, electroporation instruments and systems and methods of electroporation using these devices and systems. In some embodiments, electroporation cartridges comprise an electroporation chamber defined by an elongate body, a first electrode at a proximal end and a second electrode at a distal end of a chamber. Electroporation systems of the disclosure include one or more components including a pulse generator, compartments for placing either flow-through or single use electroporation cartridges, components for storage of cells, cooling and pre-cooling mechanisms, removably insertable modular casings having compartments for holding and arranging electroporation system and reagent components, one or more pumps for moving sample through the system, and processors and controllers.