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Abstract In the present work, we first introduce a general framework for modelling complex multiscale fluids and then focus on the derivation and analysis of a new hybrid continuum-kinetic model. In particular, we combine conservation of mass and momentum for an isentropic macroscopic model with a kinetic representation of the microscopic behavior. After introducing a small scale of interest, we compute the complex stress tensor by means of the Irving-Kirkwood formula. The latter requires an expansion of the kinetic distribution around an equilibrium state and a successive homogenization over the fast in time and small in space scale dynamics. For a new hybrid continuum-kinetic model the results of linear stability analysis indicate a conditional stability in the relevant low speed regimes and linear instability for high speed regimes for higher modes. Extensive numerical experiments confirm that the proposed multiscale model can reflect new phenomena of complex fluids not being present in standard Newtonian fluids. Consequently, the proposed general technique can be successfully used to derive new interesting systems combining the macro and micro structure of a given physical problem.