Waste management is one of the greatest contemporary challenges as the world strives for sustainable development. We set out to investigate the impact of mining waste (carboniferous rock) and organic waste (biogas digestate) on the physical properties of soils. The wastes were applied to Podzol, soil characterised by low chemical and physical quality with the particle size distribution (PSD) of loamy sand. The paper sets out to answer the question of whether a one-time application of mine and/or biogas digestate onto soil positively affects the durability of the soil structure and if the changes were permanent. For this purpose, we analysed soil texture, total organic carbon (TOC), water-stable aggregates and the mean weight diameter of water-stable aggregates (MWD). The combined addition of biogas digestate and the two types of waste improved the soil structure. The content of soil water-stable aggregates with dimensions 5–10 mm (A5–10) and 1–5 mm (A1–5) increased the MWD and the content of aggregates of diameters <1 mm (A<1) decreased. The effects of the experiment were permanent, as differences resulting from the soil treatments were still visible four years after the application. This shows that wastes, especially biogas digestate, could be successfully used in agriculture.