The Seiberg–Witten equation with multiple spinors generalises the classical Seiberg–Witten equation in dimension 3. In contrast to the classical case, the moduli space of solutions scriptM can be non‐compact due to the appearance of so‐called Fueter sections. In the absence of Fueter sections we define a signed count of points in scriptM and show its invariance under small perturbations. We then study the equation on the product of a Riemann surface and a circle, describing scriptM in terms of holomorphic data over the surface. We define analytic and algebro‐geometric compactifications of scriptM, and construct a homeomorphism between them. For a generic choice of circle‐invariant parameters of the equation, Fueter sections do not appear and scriptM is a compact Kähler manifold. After a perturbation it splits into isolated points which can be counted with signs, yielding a number independent of the initial choice of the parameters. We compute this number for surfaces of low genus.