We derive renormalised finite functional flow equations for quantum field theories in real and imaginary time that incorporate scale transformations of the renormalisation conditions, hence implementing a flowing renormalisation. The flows are manifestly finite in general non-perturbative truncation schemes also for regularisation schemes that do not implement an infrared suppression of the loops in the flow. Specifically, this formulation includes finite functional flows for the effective action with a spectral Callan-Symanzik cutoff, and therefore gives access to Lorentz invariant spectral flows. The functional setup is fully non-perturbative and allows for the spectral treatment of general theories. In particular, this includes theories that do not admit a perturbative renormalisation such as asymptotically safe theories. Finally, the application of the Lorentz invariant spectral functional renormalisation group is briefly discussed for theories ranging from real scalar and Yukawa theories to gauge theories and quantum gravity.