Tailoring the electronic and optical properties of nitride‐based alloys for optoelectronic device applications in the ultraviolet and red spectral range has attracted significant attention in recent years. Adding boron nitride (BN) to indium gallium nitride (In,Ga)N alloys can help to control the lattice mismatch between (In,Ga)N and GaN and may thus allow to reduce strain‐related defect formation. However, understanding of the impact of BN on the electronic properties of III‐N alloys, in particular the influence of experimentally observed boron atom clustering, is sparse. This work presents first‐principles calculations investigating the electronic properties of highly mismatched (B,In)N alloys with boron contents between 2% and 7%. Special attention is paid to the impact of the alloy microstructure. While the results show that the lattice constants of such alloys largely agree with lattice constants determined from a Vegard approximation, the electronic structure strongly depends on the local boron atom configuration. For instance, if boron atoms are dispersed throughout the structure and are not sharing nitrogen atoms, the band gap of (B,In)N alloys is largely unaffected and stays close to the gap of pristine InN. However, in the case of boron atom clustering, i.e., when boron atoms are sharing nitrogen atoms, the band gap can be strongly reduced, often leading to a metallic state in (B,In)N alloys. These strong band gap reductions are mainly driven by carrier localization effects in the valence band. Our calculations thus show that the electronic structure of (B,In)N alloys strongly depends on the alloy microstructure and that boron atom clustering plays an important role in understanding the electronic and optical properties of these emerging materials.