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Electronic systems with flat bands are predicted to be a fertile ground for hosting emergent phenomena including unconventional magnetism and superconductivity 1–15 , but materials that manifest this feature are rare. Here, we use scanning tunnelling microscopy to elucidate the atomically resolved electronic states and their magnetic response in the kagome magnet Co 3 Sn 2 S 2 (refs. 16–20 ). We observe a pronounced peak at the Fermi level, which we identify as arising from the kinetically frustrated kagome flat band. On increasing the magnetic field up to ±8 T, this state exhibits an anomalous magnetization-polarized many-body Zeeman shift, dominated by an orbital moment that is opposite to the field direction. Such negative magnetism is induced by spin–orbit-coupling quantum phase effects 21–25 tied to non-trivial flat band systems. We image the flat band peak, resolve the associated negative magnetism and provide its connection to the Berry curvature field, showing that Co 3 Sn 2 S 2 is a rare example of a kagome magnet where the low-energy physics can be dominated by the spin–orbit-coupled flat band.