Topology is a powerful recent concept asserting that quantum states could be globally protected against local perturbations1,2. Dissipationless topologically protected states are therefore of major fundamental interest as well as of practical importance in metrology and quantum information technology. Although topological protection can be robust theoretically, in realistic devices it is often susceptible to various dissipative mechanisms, which are difficult to study directly because of their microscopic origins. Here we use scanning nanothermometry3 to visualize and investigate the microscopic mechanisms that undermine dissipationless transport in the quantum Hall state in graphene. Simultaneous nanoscale thermal and scanning gate microscopy shows that the dissipation is governed by crosstalk between counterpropagating pairs of downstream and upstream channels that appear at graphene boundaries as a result of edge reconstruction. Instead of local Joule heating, however, the dissipation mechanism comprises two distinct and spatially separated processes. The work-generating process that we image directly, which involves elastic tunnelling of charge carriers between the quantum channels, determines the transport properties but does not generate local heat. By contrast, the heat and entropy generation process—which we visualize independently—occurs nonlocally upon resonant inelastic scattering from single atomic defects at graphene edges, and does not affect transport. Our findings provide an insight into the mechanisms that conceal the true topological protection, and suggest routes towards engineering more robust quantum states for device applications.