Developing green composites has received intense attention among the scientific community because of their ability to help alleviate the global environmental pollution challenges. This current work focused on preparing a bio-based composite material with desirable performance using renewable materials like diatomaceous earth, and polylactic acid (PLA) with poly(butanediol adipate ester) prepolymer (PBAPU) as a compatibilizer. The composites were prepared by reactive mixing using an intensive mixer. Subsequently, the effects of the PBAPU content on the structure and properties of the composites were studied. From the test results, it was revealed that increasing the PBAPU content resulted in an increasing trend in the properties of the composites. For instance, the thermal stability of the composites was improved as the PBAPU content was increased, and the best thermal stability was obtained when 20 wt% PBAPU was added. In addition, the mechanical properties test results showed that the elongation at break and impact strength of the composites increased with increasing PBAPU content. On the contrary, the tensile strength of the composites decreased with increasing PBAPU content. The scanning electron microscope images showed that the compatibility between the PLA matrix and PBAPU in the composites was improved significantly. Based on the analysis of the test results for the material's structure, morphology, thermal stability, fluidity, and other properties, it can be concluded that a bio-based composite material with desirable performance was successfully prepared.