MicroRNAs (miRNAs) impinge on the translation and stability of a wide variety of mRNAs, and play key roles in development, homeostasis and disease. The gene regulation mechanisms they instigate are largely effected through the activities and interactions of the CCR4-NOT deadenylase complex, but the molecular events that occur on target mRNAs and lead to silencing are poorly resolved. Using comparative proteomics, we observed a broad convergence of interactions of germ granule and P body mRNP components on AIN-1/GW182 and NTL-1/CNOT1 in the C. elegans embryo. We show that the miRISC progressively matures on the target mRNA from a scanning form into an effector mRNP particle by sequentially recruiting the CCR4-NOT complex, and mRNP components such as the decapping and decay, or germ granule proteins. Finally, we provide evidence for a role of intrinsically disordered proteins in embryonic miRNA-mediated silencing. Our findings define dynamic steps of effector mRNP assembly in embryonic miRNA-mediated silencing, and identify a functional continuum between germ granules and P bodies in the C. elegans embryo.