Asymptotic homogenisation is considered for problems with integral constraints imposed on a slowly varying microstructure; an insulator with an array of perfectly dielectric inclusions of slowly varying size serves as a paradigm. Although it is well-known how to handle each of these effects (integral constraints, slowly varying microstructure) independently within multiple scales analysis, additional care is needed when they are combined. Using the flux transport theorem, the multiple scales form of an integral constraint on a slowly varying domain is identified. The proposed form is applied to obtain a homogenised model for the electric potential in a dielectric composite, where the microstructure slowly varies and the integral constraint arises due to a statement of charge conservation. A comparison with multiple scales analysis of the problem with established approaches provides validation that the proposed form results in the correct homogenised model.