The strongly interacting sector in the E6 inspired composite Higgs model (E6CHM) with baryon number violation possesses SU(6)times U(1)_L global symmetry. In the weakly-coupled sector of this model the U(1)_L symmetry associated with lepton number conservation is broken down to a Z^L_2 discrete symmetry, which stabilizes the proton. Near the scale f > 10 TeV the SU(6) symmetry is broken down to its SU(5) subgroup, giving rise to a set of pseudo-Nambu-Goldstone bosons (pNGBs) that involves the SM-like Higgs doublet, a scalar coloured triplet and a SM singlet boson. Because f is so high, all baryon number violating operators are sufficiently strongly suppressed. Nevertheless, in this variant of the E6CHM the observed matter-antimatter asymmetry can be induced if CP is violated. The pNGB scalar coloured triplet plays a key role in this process and leads to a distinct signature that may be detected at the LHC in the near future.