In this paper we study the degeneration of both the cohomology and the cohomotopy Frölicher spectral sequences in a special class of complex manifolds, namely the class of compact nilmanifolds endowed with a nilpotent complex structure. Whereas the cohomotopy spectral sequence is always degenerate for such a manifold, there exist many nilpotent complex structures on compact nilmanifolds for which the classical Frölicher spectral sequence does not collapse even at the second term.