In strongly nonequilibrium Bose–Einstein condensates described by the generalized Gross–Pitaevskii equation, vortex motion becomes self-accelerated while the long-range vortex–antivortex interaction appears to be repulsive. We numerically study the impact of these rather unusual vortex properties on the dynamics of multivortex systems. We show that at strong nonequilibrium the repulsion between vortices and antivortices leads to a dramatic slowdown of their annihilation. Moreover, in finite-size samples, relaxation of multivortex systems can lead to the formation of metastable vortex–antivortex clusters, whose shape and size depend, in particular, on the sample geometry, boundary conditions and deviations from equilibrium. We further demonstrate that at strong nonequilibrium the interaction of self-accelerated vortices with inhomogeneous condensate flows can lead to generation of new vortex–antivortex pairs.