One way to reduce carbon dioxide emissions from the current heavy-duty vehicles fleet is to replace fossil fuel with renewable fuel. This can be done by blending so-called drop-in fuels into the standard diesel fuel. However, problems such as insoluble impurities may arise when the fuels are mixed. These precipitates, known as soft particles, can cause deposits in the fuel system, e.g., injectors and fuel filters, reducing the engine´s performance. The most used drop-in fuel today is biodiesel which, is blended with different concentrations. To better understand how soft particles are formed in the vehicle´s fuel system, the degradation of biodiesel blends in the engine has been investigated. This study explores biodiesel blends´ degradation process by comparing the incoming fuel with the return fuel from a modern diesel engine to investigate how the fuel is affected by this process. The engine was run using different blends of biodiesel fuel. To investigate the degradation of the biodiesel, engine tests at low, medium, and high torque at two engine speeds was performed. Fuel samples were collected before and after the engine for comparison. The tested fuels were examined with different analytical techniques. Rancimat, ion chromatography, inductively coupled plasma atomic emission spectroscopy and total acid number. A filtration test method was developed to collect the soft particles from the tested fuels. The results showed that fuel properties from the fuel return in biodiesel blends with high biodiesel content were more affected compared to lower biodiesel blends. For the lower biodiesel blends both the oxidation stability (Rancimat) and the filterability improved after passing the fuel system in the engine. While for the high biodiesel content, Rancimat and filterability were reduced. In biodiesels blends lower than 10%v/v, the change in oxidation stability was positive and around 30h and for B100 the change in oxidation stability was negative around 5 to 10 h. The filterability of blends with high biodiesel content showed that these fuels were more affected by different engine conditions, whereas B30 showed the highest variation in filtration time. Indicating that B30 is the most sensitive fuel. No big change was seen in the acid number for any biodiesel blends and a correlation was seen with biodiesel content. Further, the concentration of short chain fatty acid seems to correlate with the oxidation stability of the fuel. Increasing the level of short chain fatty acids, the oxidation stability of the fuel decreases.