Renewable fuels are essential in the field of heavy duty transportation if we are to reach a fossil-free society in the foreseeable future. However renewable diesel fuels based on fatty acid methyl ester (FAME) might face problems with degradation and with cold flow properties. From the perspective of an engine, this may cause problems in the fuel injection system, such as fuel filter clogging and injector deposits. These phenomena, especially fuel filter clogging, can be connected to gel-like soft particles, which could originate from degradation products as well as from byproducts created during biodiesel refining. In this study, soft particles from the degradation of bio-based diesel fuel were examined. The tested fuels included hydrogenated vegetable oils (HVO), rapeseed methyl ester (RME) and 10% blend of rapeseed methyl ester with standard diesel (B10). To test their potential to increase the formation of soft particles, contaminants such as water, metals and engine oil were included in the degradation methods. The formed insoluble products were analyzed with gravimetric means, scanning electron microscopy (SEM/EDX) and spectroscopy methods (FTIR). The results showed different behavior for each of the tested fuels. B10 was shown to be the most problematic, with the creation of gel-like soft particles. RME was less prone to create particles, probably due to its good solubility properties. HVO created the least sediments, possibly due to its high stability. According to the FTIR measurements, the captured insoluble sediments mainly consisted of polymerized oxidation products, acids and metal carboxylic ions. The type of metal influenced the chemical composition and the amount of insoluble sediment. Engine oil caused an increase in the amount of sediments. However the results also suggest that oil has a dampening effect for reactions between metals, water and fuels.