Modular lumbar interbody fixation systems and methods with reconstruction endplates are provided. A representative system includes: a pair of engaging plates adapted to fit between and engage the vertebral bodies, at least one engaging plate of the pair of engaging plates being a reconstruction endplate, the reconstruction endplate having a trough and configured to receive a fixing agent; and an alignment device positionable between the pair of engaging plates, the alignment device being operative to maintain a disc space between the vertebral bodies during use.