The present work investigates the linear instability of three-dimensional boundary layers in thermodynamically non-ideal regimes. As a representative fluid, we consider carbon dioxide at supercritical pressure (80 bar). The flow set-up is matched to the redesigned DLR (German Aerospace Center) experiment on cross-flow instability, with identical pressure-coefficient distribution (accelerating the flow), sweep angle and Reynolds number, at a low Mach number. The flow temperature relative to the Widom line – also known as the pseudocritical line – thus characterises the non-ideality of the flow. We consider supercritical (gas-like), subcritical (liquid-like) and transcritical (pseudoboiling) regimes, where the flow temperature remains above, below or crosses the Widom line. The stability analyses of the parabolised Navier–Stokes baseflows indicate that wall heating destabilises the flow in the supercritical regime while wall cooling stabilises both effects similar to the ideal-fluid situation but being stronger. On the contrary, wall heating/cooling exhibits reversed effects in the subcritical regime, like for an ideal liquid. In the transcritical regime, with its sharp gradients of the thermodynamic and transport properties, wall heating stabilises the flow. Most substantially, however, wall cooling provokes a changeover of the leading instability mechanism: the accelerated streamwise flow attains inflectional wall-normal profiles, and the invoked inviscid Tollmien–Schlichting instability prevails with growth rates up to one order of magnitude larger than those of the cross-flow mode. We establish a two-fold mathematical relation from the momentum equation that explains the consequence of non-ideality and wall heating/cooling. The streamwise perturbation patterns of the flows in their linear instability regime are shown by mimicking wave trains emanating from virtual point-disturbance sources. From the viewpoint of keeping laminar flows, the transcritical thermodynamic state with a cooling wall must be avoided.