The Jacobian matrix of a dynamical system describes its response to perturbations. Conversely, one can estimate the Jacobian matrix by carefully monitoring how the system responds to environmental noise. We present a closed-form analytical solution for the calculation of a system’s Jacobian from a time series. Being able to access the Jacobian enables a broad range of mathematical analyses by which deeper insights into the system can be gained. Here we consider in particular the computation of the leading Jacobian eigenvalue as an early warning signal for critical transitions. To illustrate this approach, we apply it to ecological meta-foodweb models, which are strongly nonlinear dynamical multi-layer networks. Our analysis shows that accurate results can be obtained, although the data demand of the method is still high.