Upcoming neutrino experiments will not only constrain oscillation parameters with an unprecedented precision, but will also search for physics beyond the Standard Model. ORCA is the atmospheric neutrino detector of the KM3NeT telescope, sensitive to energies from a few GeV to around 100 GeV and with a large potential to explore new physics. A high-purity neutrino sample from data taken with the first six detection units deployed has been selected. The sample has been analysed to probe sub-dominant effects in the oscillation patterns of atmospheric neutrinos propagating through the Earth, as invisible neutrino decay and Non-Standard Interactions. In this contribution, the boundaries obtained for the decay parameter, $\alpha_3=m_3/\tau_3$, and the flavour violating interaction parameters, $\epsilon_{\alpha\beta}$, are presented together with future sensitivity perspectives after ten years of data taking with the final ORCA configuration of 115 detection units.