Cell-free systems have emerged as a powerful platform for protein production, characterization, and bottom-up construction of artificial cells, offering direct control over biochemical environments. However, achieving high-throughput and iterative design–build–test cycles requires advanced strategies beyond conventional methods. Microfluidic technologies address these challenges by enabling miniaturization, automation, and exceptional control over reaction conditions. The integration of cell-free systems with microfluidics has unlocked new capabilities by enabling high-throughput assays, long-lived reactions in continuous-flow systems, and the generation of liposome-based artificial cells. This review highlights recent advances at this interface, focusing on microfluidic strategies for protein characterization, gene regulatory studies, and the bottom-up construction of artificial cells exhibiting life-like functions.