Topological defects, such as vortices and disclinations, play a crucial role in spatiotemporal organization of equilibrium and non-equilibrium systems. The defect immobilization or pinning is a formidable challenge in the context of the out-of-equilibrium system, like a living liquid crystal, a suspension of swimming bacteria in lyotropic liquid crystal. Here we control the emerged topological defects in a living liquid crystal by arrays of 3D-printed microscopic obstacles (pillars). Our studies show that while −1/2 defects may be easily immobilized by the pillars, +1/2 defects remain motile. Due to attraction between oppositely charged defects, positive defects remain in the vicinity of pinned negative defects, and the diffusivity of positive defects is significantly reduced. Experimental findings are rationalized by computational modeling of living liquid crystals. Our results provide insight into the engineering of active systems via targeted immobilization of topological defects.