Reliable quantification of 3D results obtained by X-ray energy-dispersive spectroscopy (XEDS) tomography is currently hampered by the presence of shadowing effects and poor spatial resolution. Here, a method is presented which overcomes these problems by synergistically combining quantified XEDS data and high angle annular dark field-scanning transmission electron microscopy tomography. As a proof of principle, the approach is applied to characterize a complex Au/Ag nanorattle obtained through a galvanic replacement reaction. However, the technique that is proposed here is widely applicable to a broad range of nanostructures.