Novel approaches to genome engineering are crucial to rapidly advance the capabilities of strain engineering and synthetic biology. With ongoing developments in DNA editing techniques, researchers have begun to engineer organisms at higher throughput and can now perform multiple genome modifications simultaneously. As laboratory automation becomes more accessible, workflows are being transferred to robot-assisted platforms, enabling large-scale and highly parallelized genome editing campaigns. These platforms play a key role in fully utilizing the potential of modern molecular biology tools. Here, we review recent developments in technologies for high-throughput, multiplexed, and automated strain engineering in prokaryotic and eukaryotic organisms.