Abstract The similar densities of dark matter and baryons in the universe imply that they might arise from the same ultraviolet model. The B-Mesogenesis, which assumes dark matter is charged under the baryon number, attempts to simultaneously explain the origin of baryon asymmetry and dark matter in the universe. In particular, the B-Mesogenesis might induce bottom-baryon decays into invisible or semi-invisible final states, which provide a distinctive signal for probing this scenario. In this work, we systematically study the invisible decays of bottom baryons into dark matters, and semi-invisible decays of bottom baryons into a meson or a photon together with a dark matter particle. In particular, the fully invisible decay can explore the stable particles in B-Mesogenesis. Some QCD-based frameworks are used to calculate the hadronic matrix elements under the B-Mesogenesis model. We estimate the constraints on the Wilson coefficients or the product of some new physics couplings with the Wilson coefficients by the semi-invisible and invisible decays of bottom baryons at future colliders. Content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. Article funded by SCOAP3 and published under licence by Chinese Physical Society and the Institute of High Energy Physics of the Chinese Academy of Science and the Institute of Modern Physics of the Chinese Academy of Sciences and IOP Publishing Ltd.