Although different types of biodiesel are marketed worldwide, studies on their environmental impact are scarce. Therefore, we selected pure biodiesels (B100) from rapeseed (BR), sunflower (BF), and soybean (BS) to mimic their contamination of sandy loam soil and then studied their biodegradation by the soil microcosms. All the biodiesel samples presented significant values (p < 0.05) of CO2 release. The fatty acid profiles revealed that they all had high rates of degradation. After 56 days of study, the BR- and BF-contaminated samples had the most altered microbial profile, presenting a similarity of 75% with the uncontaminated sample. The results showed the high biodegradable potential of these three types of biodiesel, indicating that their compositions favored the degradation process. However, the high CO2 level released by the mineralization of these biocomposites and the alteration in the soil microbial profile can be worrying factors. This is the first work to evaluate the biodegradability of these three types of biodiesel, the microbial profile of soil contaminated by each type, and their emission of greenhouse gases.