We report the alignment of In nanocrystals on top of linear InGaAs quantum dot (QD) arrays formed by self-organized anisotropic strain engineering on GaAs (100) by molecular beam epitaxy. The alignment is independent of a thin GaAs cap layer on the QDs revealing its origin is due to local strain recognition. This enables nanometer-scale precise lateral and vertical site registration between the QDs and the In nanocrystals and arrays in a single self-organizing formation process. The plasmon resonance of the In nanocrystals overlaps with the high-energy side of the QD emission leading to clear modification of the QD emission spectrum