We extend the multi-purpose Monte Carlo event generator Sherpa to include processes in deeply inelastic lepton–nucleon scattering. Hadronic final states in this kinematical setting are characterised by the presence of multiple kinematical scales, which were up to now accounted for only by specific resummations in individual kinematical regions. Using an extension of the recently introduced method for merging truncated parton showers with higher-order tree-level matrix elements, it is possible to obtain predictions which are reliable in all kinematical limits. Different hadronic final states, defined by jets or individual hadrons, in deep-inelastic scattering are analysed and the corresponding results are compared to HERA data. The various sources of theoretical uncertainties of the approach are discussed and quantified. The extension to deeply inelastic processes provides the opportunity to validate the merging of matrix elements and parton showers in multi-scale kinematics inaccessible in other collider environments. It also allows to use HERA data on hadronic final states in the tuning of hadronisation models.