The history of dark universe physics can be traced from processes in the very early universe to the modern dominance of dark matter and energy. Here, we review the possible nontrivial role of strong interactions in cosmological effects of new physics. In the case of ordinary QCD interaction, the existence of new stable colored particles such as new stable quarks leads to new exotic forms of matter, some of which can be candidates for dark matter. New QCD-like strong interactions lead to new stable composite candidates bound by QCD-like confinement. We put special emphasis on the effects of interaction between new stable hadrons and ordinary matter, formation of anomalous forms of cosmic rays and exotic forms of matter, like stable fractionally charged particles. The possible correlation of these effects with high energy neutrino and cosmic ray signatures opens the way to study new physics of strong interactions by its indirect multi-messenger astrophysical probes.