Colloidal dispersions in liquid crystals can serve as a soft-matter toolkit for the self-assembly of composite materials with pre-engineered properties and structures that are highly dependent on particle-induced topological defects. Here, we demonstrate that bulk and surface defects in nematic fluids can be patterned by tuning the topology of colloidal particles dispersed in them. In particular, by taking advantage of two-photon photopolymerization techniques to make knot-shaped microparticles, we show that the interplay of the topologies of the knotted particles, the nematic field and the induced defects leads to knotted, linked and other topologically non-trivial field configurations. These structures match theoretical predictions made on the basis of the minimization of the elastic free energy and satisfy topological constraints. Our approach may find uses in self-assembled topological superstructures of knotted particles linked by nematic fields, in topological scaffolds supporting the decoration of defect networks with nanoparticles, and in modelling other physical systems exhibiting topologically analogous phenomena.