Electronic systems with flat bands are predicted to be a fertile ground for hosting emergent phenomena including unconventional magnetism and superconductivity1-15, 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 Co3Sn2S2 (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 effects21-25 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 Co3Sn2S2 is a rare example of a kagome magnet where the low-energy physics can be dominated by the spin-orbit-coupled flat band.