Atom optics demonstrates optical phenomena with coherent matter waves, providing a foundational connection between light and matter. Significant advances in optics have followed the realization of structured light fields hosting complex singularities and topologically non-trivial characteristics. However, analogous studies are still in their infancy in the field of atom optics. Here, we investigate and experimentally create knotted quantum wavefunctions in spinor Bose–Einstein condensates which display non-trivial topologies. In our work we construct coordinated orbital and spin rotations of the atomic wavefunction, engineering a variety of discrete symmetries in the combined spin and orbital degrees of freedom. The structured wavefunctions that we create map to the surface of a torus to form torus knots, Möbius strips, and a twice-linked Solomon’s knot. In this paper we demonstrate close connections between the symmetries and underlying topologies of multicomponent atomic systems and of vector optical fields—a realization of topological atom-optics.