Metals exert important functions in the chloroplast of plants, where they act as cofactors and catalysts in the photosynthetic electron transport chain. In particular, manganese (Mn) has a key function because of its indispensable role in the water-splitting reaction of photosystem II (PSII). More and better knowledge is required on how the various complexes of PSII are affected in response to, for example, nutritional disorders and other environmental stress conditions. We here present, to our knowledge, a new method that allows the analysis of metal binding in intact photosynthetic complexes of barley (Hordeum vulgare) thylakoids. The method is based on size exclusion chromatography coupled to inductively coupled plasma triple-quadrupole mass spectrometry. Proper fractionation of PSII super- and subcomplexes was achieved by critical selection of elution buffers, detergents for protein solubilization, and stabilizers to maintain complex integrity. The applicability of the method was shown by quantification of Mn binding in PSII from thylakoids of two barley genotypes with contrasting Mn efficiency exposed to increasing levels of Mn deficiency. The amount of PSII supercomplexes was drastically reduced in response to Mn deficiency. The Mn efficient genotype bound significantly more Mn per unit of PSII under control and mild Mn deficiency conditions than the inefficient genotype, despite having lower or similar total leaf Mn concentrations. It is concluded that the new method facilitates studies of the internal use of Mn and other biometals in various PSII complexes as well as their relative dynamics according to changes in environmental conditions.