This paper describes an adaptive preconditioner for numerical continuation of incompressible Navier–Stokes flows based on Stokes preconditioning [42] which has been used successfully in studies of pattern formation in convection. The preconditioner takes the form of the Helmholtz operator I−∆tL which maps the identity (no preconditioner) for ∆t ≪ 1 to Laplacian preconditioning for ∆t ≫ 1. It is built on a first order Euler time-discretization scheme and is part of the family of matrix-free methods. The preconditioner is tested on two fluid configurations: three-dimensional doubly diffusive convection and a two-dimensional projection of a shear flow. In the former case, it is found that Stokes preconditioning is more efficient for ∆t = $\mathcal{O}$(1), away from the values used in the literature. In the latter case, the simple use of the preconditioner is not sufficient and it is necessary to split the system of equations into two subsystems which are solved simultaneously using two different preconditioners, one of which is parameter dependent. Due to the nature of these applications and the flexibility of the approach described, this preconditioner is expected to help in a wide range of applications.