Early embryos are the epitome of self-organization. Following the cell cycle oscillator, their internal structure is continuously re-organized into precise patterns at remarkable speeds. For example, the mm-sized egg of the frog Xenopus Laevis, divides every 30 minutes in equally-sized cells. Physical processes such as autocatalytic growth, active transport, and reaction- diffusion can allow these embryos to keep up with fast cell cycle times, however their understanding in early development remains largely elusive. Here, we present recent data from experiments of in vitro cytoplasmic extract obtained from frog egg and exhibiting cell-free division. We show that the properties of the cell cycle oscillator regulate the pattern of cytoplasmic compartments. Specifically, by perturbing the oscillator, we establish that the interface of cytoplasmic compartments is unstable. We demonstrate that such instability emerges from competing waves of autocatalytic microtubule growth, and can generate compartment fusion, strongly affecting the embryonic early pattern formation. Altogether, our results propose that the cell cycle oscillator plays a critical role in partitioning the cytoplasm of early embryos, keeping the dynamic instability of cytoplasmic compartments at bay.