The increasing demand for lithium-ion batteries requires constant improvements in the areas of production and recycling to reduce their environmental impact. In this context, this work presents a method for structuring carbon black aggregates by adding colloidal silica via a spray flame with the goal of opening up more choices for polymeric binders. The main focus of this research lies in the multiscale characterization of the aggregate properties via small-angle X-ray scattering, analytical disc centrifugation and electron microscopy. The results show successful formation of sinter-bridges between silica and carbon black leading to an increase in hydrodynamic aggregate diameter from 201 nm to up to 357 nm, with no significant changes in primary particle properties. However, segregation and coalescence of silica particles was identified for higher mass ratios of silica to carbon black, resulting in a reduction in the homogeneity of the hetero-aggregates. This effect was particularly evident for silica particles with larger diameters of 60 nm. Consequently, optimal conditions for hetero-aggregation were identified at mass ratios below 1 and particle sizes around 10 nm, at which homogenous distributions of silica within the carbon black structure were achieved. The results emphasise the general applicability of hetero-aggregation via spray flames with possible applications as battery materials.