Nanotechnology has acquired significance in dental applications, but its safety regarding human health is still questionable due to the chemicals utilized during various synthesis procedures. Titanium nanoparticles were produced by three novel routes, including Bacillus subtilis, Cassia fistula and hydrothermal heating, and then characterized for shape, phase state, size, surface roughness, elemental composition, texture and morphology by SEM, TEM, XRD, AFM, DRS, DLS and FTIR. These novel titanium nanoparticles were tested for cytotoxicity through the MTT assay. L929 mouse fibroblast cells were used to test the cytotoxicity of the prepared titanium nanoparticles. Cell suspension of 10% DMEM with 1 × 104 cells was seeded in a 96-well plate and incubated. Titanium nanoparticles were used in a 1 mg/mL concentration. Control (water) and titanium nanoparticles stock solutions were prepared with 28 microliters of MTT dye and poured into each well, incubated at 37 °C for 2 h. Readings were recorded on day 1, day 15, day 31, day 41 and day 51. The results concluded that titanium nanoparticles produced by Bacillus subtilis remained non-cytotoxic because cell viability was >90%. Titanium nanoparticles produced by Cassia fistula revealed mild cytotoxicity on day 1, day 15 and day 31 because cell viability was 60–90%, while moderate cytotoxicity was found at day 41 and day 51, as cell viability was 30–60%. Titanium nanoparticles produced by hydrothermal heating depicted mild cytotoxicity on day 1 and day 15; moderate cytotoxicity on day 31; and severe cytotoxicity on day 41 and day 51 because cell viability was less than 30% (p < 0.001). The current study concluded that novel titanium nanoparticles prepared by Bacillus subtilis were the safest, more sustainable and most biocompatible for future restorative nano-dentistry purposes.