The multilevel Monte Carlo (MLMC) method has proven to be an effective variance-reduction statistical method for Uncertainty quantification in PDE models. It combines approximations at different levels of accuracy using a hierarchy of meshes in a similar way as multigrid. The generation of body-fitted mesh hierarchies is only possible for simple geometries. On top of that, MLMC for random domains involves the generation of a mesh for every sample. Instead, here we consider the use of embedded methods which make use of simple background meshes of an artificial domain (a bounding-box) for which it is easy to define a mesh hierarchy, thus eliminating the need of body-fitted unstructured meshes, but can produce ill-conditioned discrete problems. To avoid this complication, we consider the recent aggregated finite element method (AgFEM). In particular, we design an embedded MLMC framework for (geometrically and topologically) random domains implicitly defined through a random level-set function, which makes use of a set of hierarchical background meshes and the AgFEM. Performance predictions from existing theory are verified statistically in three numerical experiments, namely the solution of the Poisson equation on a circular domain of random radius, the solution of the Poisson equation on a topologically identical but more complex domain, and the solution of a heat-transfer problem in a domain that has geometric and topological uncertainties. Finally, the use of AgFE is statistically demonstrated to be crucial for complex and uncertain geometries in terms of robustness and computational cost. Date: November 28, 2019.