Manganese oxide species have been frequently used for Fenton catalyst design, but their role in reaction with hydrogen peroxide (H2O2) is still in debate. We here revealed the different routes of manganese oxide/H2O2 interactions occurring at bulk surfaces to that at nanopore-confined surfaces, which have been overlooked in literatures. Briefly, particulate manganese oxide species cause a fast H2O2 decomposition influenced by the valence of manganese and solution pH, but without generation of reactive oxygen species (•OH, •O2-, or 1O2) for water treatment; in contrast, manganese oxide/H2O2 interaction under nanopore confinement (ca. 1 nm) led to the production of radicals (mainly •OH and •O2-) and the removal of organic pollutants. We gained insights into the differed reaction routes based on experimental and computational study. Our findings provide caveats on the indiscriminate pursuit of manganese in Fenton catalyst development, against a nullified H2O2 decomposition and impractically slow radical production.