Methods and systems are presented for upgrading non-volatile memories (NVMs) of controllers in a storage system. One method includes operations for taking a second controller off-line, wherein NVMs in first and second controllers are initially mirrored in a first format, with the first controller active and the second controller as standby. The method includes reformatting the second NVM in the second controller to a second format, and blocking handling of IOs at the first controller after reformatting of the second NVM is complete. The method includes migrating metadata to the second NVM from the first NVM, and bringing the second controller back on-line as standby. The method includes failing over to the second controller, and reformatting the first NVM to the second format. The method includes updating metadata in the first NVM to mirror metadata in the second NVM, and bringing the first controller back on-line in standby.