Non-standard interactions of neutrinos arising in many beyond the Standard Model physics models can significantly alter matter effects in atmospheric neutrino propagation through the Earth. In this paper, a search for deviations from the prediction of the standard 3-flavour atmospheric neutrino oscillations using the data taken by the ANTARES neutrino telescope is presented. Ten years of atmospheric neutrino data collected from 2007 to 2016, with energies in the range ∼[5 − 10 4 ] GeV, have been analysed. As a result, a log-likelihood ratio test yields best-fit values of the dimensionless coefficients that quantify the strength of non-standard interactions between the neutrino flavours, namely, ε µτ and ε τ τ , which are non-zero at the 1.7σ and 1.6σ level for the normal (NO) and inverted (IO) mass orderings, respectively. While the best-fit values ε µτ = (−1.3 +1.8 −2.0 ) × 10 −3 (NO) and (1.3 +1.9 −1.8 ) × 10 −3 (IO) are compatible with zero within its 68% C.L., the values of ε τ τ = (3.2 +1.4 −0.8 ) × 10 −2 (NO) and (−3.2 +1.9 −1.1 ) × 10 −2 (IO) are compatible with zero only within its 95% C.L. range. The constraint on ε µτ is slightly more stringent than current bounds from other experiments and it further restrains the strength of possible non-standard interactions in the µ − τ sector.