Soy-based yoghurt alternatives were highly requested by consumers over the last few years. However, their texture does not always fulfil consumers’ demands as such yoghurt alternatives are often perceived as too firm or too soft, sandy, or fibrous. In order to improve the texture, fibres, for example, in the form of microgel particles (MGP), can be added to the soy matrix. MGP are expected to interact with soy proteins, creating different microstructures and, thus, different gel properties after fermentation. In this study, pectin-based MGP were added in different sizes and concentrations, and the soy gel properties after fermentation were characterised. It was found that the addition of 1 wt.% MGP influenced neither the flow behaviour nor the tribological/lubrication properties of the soy matrix, regardless of the MGP size. However, at higher MGP concentrations (3 and 5 wt.%), the viscosity and yield stress were reduced, the gel strength and cross-linking density decreased, and the water-holding capacity was reduced. At 5 wt.%, strong and visible phase separation occurred. Thus, it can be concluded that apple pectin-based MGP serve as inactive fillers in fermented soy protein matrices. They can, therefore, be used to weaken the gel matrix purposely to create novel microstructures.