Manganese (Mn) toxicity-induced leaf chlorosis limits crop production in acidic soils, but its underlying mechanisms remain unknown. The effects of excessive Mn on chlorophyll (Chl) biosynthesis in sugarcane (Saccharum officinarum L.) leaves were investigated. Under Mn treatment, Chl concentration decreased with Mn accumulation and chlorosis appeared in expanding leaves. Before that, levels of the initial Chl precursor 5-aminolevulinic acid (ALA) and its downstream intermediates decreased, whereas magnesium-protoporphyrin IX monomethyl ester (MgPME) accumulated. Overaccumulation of Mn in leaves downregulated the ALA biosynthetic gene GluTR (encoding glutamyl-tRNA reductase) and MgPME conversion gene MgPMEC (encoding MgPME cyclase), upregulated the ALA biosynthesis inhibitor FLU (encoding FLUORESCENT), but had no significant effect on the expression of other Chl biosynthetic genes. The above Mn-induced changes of Chl precursors and expression of corresponding genes commenced before the Chl decline and leaf chlorosis, and were reversed by ALA supplementation. Thus, excessive Mn-induced chlorosis in sugarcane is mediated by a Chl-biosynthesis disorder resulting from the inhibition of ALA synthesis and MgPME conversion.