ABSTRACT Weak gravitational lensing convergence peaks, the local maxima in weak lensing convergence maps, have been shown to contain valuable cosmological information complementary to commonly used two-point statistics. To exploit the full power of weak lensing for cosmology, we must model baryonic feedback processes because these reshape the matter distribution on non-linear and mildly non-linear scales. We study the impact of baryonic physics on the number density of weak lensing peaks using the FLAMINGO cosmological hydrodynamical simulation suite. We generate ray-traced full-sky convergence maps mimicking the characteristics of a Stage IV weak lensing survey. We compare the number densities of peaks in simulations that have been calibrated to reproduce the observed galaxy mass function and cluster gas fraction or to match a shifted version of these, and that use either thermally driven or jet active galactic nucleus feedback. We show that the differences induced by realistic baryonic feedback prescriptions (typically 5–30 per cent for κ = 0.1–0.4) are smaller than those induced by reasonable variations in cosmological parameters (20–60 per cent for κ = 0.1–0.4) but must be modelled carefully to obtain unbiased results. The reasons behind these differences can be understood by considering the impact of feedback on halo masses, or by considering the impact of different cosmological parameters on the halo mass function. Our analysis demonstrates that, for the range of models we investigated, the baryonic suppression is insensitive to changes in cosmology up to κ ≈ 0.4 and that the higher κ regime is dominated by Poisson noise and cosmic variance.