The effect of pressure gradients on the stability of creeping flows of Newtonian fluids in channels lined with an incompressible and impermeable neo-Hookean material is examined in this work. Three different configurations are considered: (i) pressure-driven flow between a rigid wall and a wall lined with a neo-Hookean material; (ii) pressure-driven flow between neo-Hookean-lined walls; and (iii) combined Couette–Poiseuille flow between a rigid wall and a neo-Hookean-lined wall. In each case, a first normal stress difference whose magnitude depends on depth arises in the base state for the solid, and linear stability analysis reveals that this leads to a short-wave instability which is removed by the presence of interfacial tension. For sufficiently thick solids, low-wavenumber modes become unstable first as the applied strain increases above a critical value, whereas for sufficiently thin solids, high-wavenumber modes becomes unstable first. Comparison of the dimensionless critical strains shows that configurations (i) and (ii) are more difficult to destabilize than Couette flow past a neo-Hookean solid. For configuration (iii), the nonlinear elasticity of the solid leads to two physically distinct critical conditions, in contrast to what happens when a linear elastic material is used. The mechanisms underlying the behaviour of the critical strains are explained through an analysis of the interfacial boundary conditions.