The first direct, model-independent measurement is presented of the modulus of the Cabibbo–Kobayashi–Maskawa (CKM) matrix elements |η|Vtb, |η|Vtd, and |η|Vts, in final states enriched in single top quark t-channel events. The analysis uses proton-proton collision data from the LHC, collected during 2016 by the CMS experiment, at a centre-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 35.9 fb−1. Processes directly sensitive to these matrix elements are considered at both the production and decay vertices of the top quark. In the standard model hypothesis of CKM unitarity, a lower limit of |η|Vtb>0.970 is measured at the 95% confidence level. Several theories beyond the standard model are considered, and by releasing all constraints among the involved parameters, the values |η|Vtb=0.988±0.024, and |η|Vtd2+|η|Vts2=0.06±0.06, where the uncertainties include both statistical and systematic components, are measured.