Abstract Here, chemically powered and magnetically guided janus m agneto‐ f luorescent d ual‐ e ngine n anobots (MFDEN) that harvest their energy from the reactions with two different fuels are reported. The Mg‐Fe 3 O 4 Janus nanobots prepared by depositing Fe 3 O 4 hemispherical layer on Mg nanoparticles are propelled efficiently by the thrust of oxygen bubble generated from the reactions of Fe 3 O 4 in H 2 O 2 media, and by hydrogen bubble produced at the partial Mg opening in aqueous media. High speeds and long lifetimes are achieved in complex biological media with H 2 O 2 or with NaHCO 3 , respectively. For the first time, this study demonstrates the utility of nanobots for efficient isolation of trophoblastic cells from blood. Considering the extreme rarity of these cells in blood, efficient technique that enriches sufficient cells rapidly and with specificity is desired. The nanobots exhibit excellent capture efficiency of almost 100%, both in serum and whole blood for trophoblastic Be‐Wo cells. Furthermore, the high capture efficiency is achieved in 5 min. Feasibility of obtaining an isolated cell based diagnosis from whole blood is demonstrated. Although determining the exact sensitivity and specificity will require more data, this study supports the potential of the multiple fuel‐powered nanorobots for clinical translation of circulating fetal cell based non‐invasive prenatal testing.