We introduce a new class of spatial Cox processes driven by a Hilbert-valued random log-intensity. We adopt a parametric framework in the spectral domain, to estimate its spatial functional correlation structure. Specifically, we consider a spectral functional, approach based on the periodogram operator, inspired on Whittle estimation methodology. Strong consistency of the parametric estimator is proved in the linear case. We illustrate this property in a simulation study under a Gaussian first-order Spatial Autoregressive Hilbertian scenario for the log-intensity model. Our method is applied to the spatial functional prediction of respiratory disease mortality in the Spanish Iberian Peninsula, in the period 1980–2015.