We show that color-breaking vacua may develop at high temperature in the Mini-Split SUSY scenario. This can lead to a nontrivial cosmological history of the universe, including strong first order phase transitions and domain wall production. Given the typical PeV energy scale associated with Mini-Split SUSY models, a stochastic gravitational wave background at frequencies around 100 Hz is expected. We study the potential for detection of such a signal in future gravitational wave experiments.