In this paper, we show that geometric functionals (e.g., excursion area, boundary length) evaluated on excursion sets of sphere-cross-time long memory random fields can exhibit fractional cointegration, meaning that some of their linear combinations have shorter memory than the original vector. These results prove the existence of long-run equilibrium relationships between functionals evaluated at different threshold values; as a statistical application, we discuss a frequency-domain estimator for the Adler-Taylor metric factor, i.e., the variance of the field's gradient. Our results are illustrated also by Monte Carlo simulations.