The stability properties of selected flow configurations, usually denoted as base flows, can be significantly altered by small modifications of the flow, which can be caused, for instance, by a non-intrusive passive control. This aspect is amply demonstrated in the literature by ad hoc sensitivity studies which, however, focus on configurations characterised by a steady base flow. Nevertheless, several flow configurations of interest are characterised by a time-periodic base flow. To this purpose, we propose here an original theoretical framework suitable to quantify the effects of base-flow variations in the stability properties of saturated time-periodic limit cycles. In particular, starting from a Floquet analysis of the linearised Navier–Stokes equations and using adjoint methods, it is possible to estimate the variation of a selected Floquet exponent caused by a generic structural perturbation of the base-flow equations. This link is expressed concisely using the adjoint operators coming from the analysis, and the final result, when applied to spatially localised disturbances, is used to build spatial sensitivity and control maps. These maps identify the regions of the flow where the placement of a infinitesimal small object produces the largest effect on the Floquet exponent and may also provide a quantification of this effect. Such analysis brings useful insights both for passive control strategies and for further characterising the investigated instability. As an example of application, the proposed analysis is applied here to the three-dimensional flow instabilities in the wake past a circular cylinder. This is a classical problem which has been widely studied in the literature. Nevertheless, by applying the proposed analysis we derive original results comprising a further characterisation of the instability and related control maps. We finally show that the control maps obtained here are in very good agreement with control experiments documented in the literature.