Bioengineered spider silks are a biomaterial with great potential for applications in biomedicine. They are biocompatible,biodegradable and can self-assemble into films, hydrogels, scaffolds, fibers, capsules and spheres. A novel, tag-free, bioengineered spider silk named MS2(9x) was constructed. It is a 9-mer of the consensus motif derived from MaSp2–the spidroin of Nephila clavipes dragline silk. Thermal and acidic extraction methods were used to purify MS2(9x). Both purification protocols gave a similar quantity and quality of soluble silk; however, they differed in the secondary structure and zeta potential value. Spheres made of these purified variants differed with regard to critical features such as particle size, morphology, zeta potential and drug loading. Independent of the purification method, neither variant of the MS2(9x) spheres was cytotoxic, which confirmed that both methods can be used for biomedical applications. However, this study highlights the impact that the applied purification method has on the further biomaterial properties.