Protein-protein interactions (PPIs) are fundamental to understanding cellular processes, serving as the cornerstone of biological signaling, structural organization, and metabolic regulation. However, capturing PPIs in living organisms remains a significant challenge, particularly in complex and compartmentalized cellular environments. Research in this area has been greatly accelerated by the invention of proximity labeling (PL) techniques. By employing engineered enzymes capable of tagging proteins and other molecules in vivo, PL allows real-time mapping of biomolecular interactions within native environments. In plants, the implementation of PL presents unique challenges but has nonetheless emerged as a powerful tool. Here, we summarize the mechanisms, strengths, and weaknesses of different enzyme-based PL methods. We also highlight key considerations to optimize PL experiments in plants and propose targets for development to further improve their efficiency and flexibility.