Manganese (Mn) is an essential metal for plant growth. The most important Mn-containing enzyme is the Mn4CaO5 cluster that catalyzes water oxidation in Photosystem II. Mn deficiency primarily affects photosynthesis, while Mn excess is generally toxic. Here, we studied Mn excess and deficiency in the liverwort Marchantia polymorpha, an emerging model ideally suited for analysis of metal stress since it accumulates rapidly toxic substances due to the absence of well-developed vascular and radicular systems and a reduced cuticle. We established growth conditions for Mn excess and deficiency and analyzed the metal content in thalli and isolated chloroplasts. In vivo super-resolution fluorescence microscopy and transmission electron microscopy revealed changes in the organization of the thylakoid membrane under Mn excess and deficiency. Both Mn excess and Mn deficiency increased the stacking of the thylakoid membrane. We investigated photosynthetic performance by measuring chlorophyll fluorescence at room temperature and 77 K, measuring P700 absorbance, and studying the susceptibility of thalli to photoinhibition. Non-optimal Mn concentrations changed the ratio of photosystem I to photosystem II. Upon Mn deficiency, higher non-photochemical quenching was observed, electron donation to photosystem I was favored, and photosystem II was less susceptible to photoinhibition. Mn deficiency seemed to favor cyclic electron flow around photosystem I, thereby protecting photosystem II in high light. The results presented here suggest an important role of Mn for the organization of the thylakoid membrane and photosynthetic electron transport.