To study the critical Casimir force between chemically structured boundaries immersed in a binary mixture at its demixing transition, we consider a strip of Ising spins subject to alternating fixed spin boundary conditions. The system exhibits a boundary induced phase transition as function of the relative amount of up and down boundary spins. This transition is associated with a sign change of the asymptotic force and a diverging correlation length that sets the scale for the crossover between different universal force amplitudes. Using conformal field theory and a mapping to Majorana fermions, we obtain the universal scaling function of this crossover, and the force at short distances.