In the formulation of stability of fluid flow through channels and tubes with deformable walls, while the fluid is naturally treated in an Eulerian framework, the solid can be treated either in a Lagrangian or Eulerian framework. A consistent formulation, then, should yield results that are independent of the chosen framework. Previous studies have demonstrated this consistency for the stability of plane Couette flow past a deformable solid layer modelled as a neo-Hookean solid, in the creeping-flow limit. However, a similar exercise carried out in the creeping-flow limit for the stability of pressure-driven flow in a neo-Hookean tube shows that while the flow is stable in the Lagrangian formulation, it is unstable in the existing Eulerian formulation. The present work resolves this discrepancy by presenting consistent Lagrangian and Eulerian frameworks for performing stability analyses in flow through deformable tubes and channels. The resolution is achieved by making important modifications to the Lagrangian formulation to make it fundamentally consistent, as well as by proposing a proper formulation for the neo-Hookean constitutive relation in the Eulerian framework. In the neo-Hookean model, the Cauchy stress tensor in the solid is proportional to the Finger tensor. We demonstrate that the neo-Hookean constitutive model within the Eulerian formulation used in the previous studies is a special case of the Mooney–Rivlin solid, with the Cauchy stress tensor being proportional to the inverse of the Finger tensor unlike in a true neo-Hookean solid. Remarkably, for plane Couette flow subjected to two-dimensional perturbations, there is perfect agreement between the results obtained using earlier Eulerian and Lagrangian formulations despite the crucial difference in the constitutive relation owing to the rather simple kinematics of the base state. However, the consequences are drastic for pressure-driven flow in a tube even for axisymmetric disturbances. We propose a consistent neo-Hookean constitutive relation in the Eulerian framework, which yields results that are in perfect agreement with the results from the Lagrangian formulation for both plane Couette and tube flows at arbitrary Reynolds number. The present study thus provides an unambiguous formulation for carrying out stability analyses in flow through deformable channels and tubes. We further show that unlike plane Couette flow and Hagen–Poiseuille flow in rigid-walled conduits where there is a remarkable similarity in the linear stability characteristics between these two flows, the stability behaviour for these two flows is very different when the walls are deformable. The instability of plane Couette flow past a deformable wall is very robust and is not sensitive to the constitutive nature of the solid, but the stability of pressure-driven flow in a deformable tube is rather sensitive to the constitutive nature of the deformable solid, especially at low Reynolds number.