We consider an infinite balls-in-boxes occupancy scheme with boxes organised in nested hierarchy, and random probabilities of boxes defined in terms of iterated fragmentation of a unit mass. We obtain a multivariate functional limit theorem for the cumulative occupancy counts as the number of balls approaches infinity. In the case of fragmentation driven by a homogeneous residual allocation model our result generalises the functional central limit theorem for the block counts in Ewens' and more general regenerative partitions.