Cyanobacteria, also known as blue-green algae, are ubiquitous organisms on the planet. They contain tremendous protein machineries that are of interest to the biotechnology indus-try and beyond. Recently, the number of annotated cyanobacterial genomes has expanded, enabling structural studies on known gene-coded proteins to accelerate. This review fo-cuses on the advances in mass spectrometry (MS) that have enabled structural proteomics studies to be performed on the proteins and protein complexes within cyanobacteria. The review also showcases examples whereby MS has revealed critical mechanistic information behind how these remarkable machines within cyanobacteria function.