Photosynthesis relies on a dynamic network of protein-protein interactions that adapt to fluctuating light conditions. We present an XL-MS pipeline applied directly to functional thylakoid membranes from Arabidopsis thaliana and Spinacia oleracea. By combining PhoX crosslinker with the amphiphilic salt TMPAC, we captured reproducible structural insights into photosynthetic protein complexes while maintaining photosynthetic activity during crosslinking. The approach enables detection of hundreds of unique crosslinks within three days, expanding thylakoid protein interaction maps, and providing structural models of known and novel complexes. This study demonstrates the feasibility of probing functional photosynthetic membranes with XL-MS, paving the way for integrative analyses of dynamic organellar networks.