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Antimicrobial resistance (AMR) has become a crucial global health issue. Antibiotic-resistant bacteria can survive after antibiotic treatments, lowering drug efficacy and increasing lethal risks. A microfluidic water-in-oil emulsion droplet system can entrap microorganisms and antibiotics within the tiny bioreactor, separate from the surroundings, enabling independent assays that can be performed in a high-throughput manner. This study presents the development of a label-free dielectrophoresis (DEP)-based microfluidic platform to sort droplets that co-encapsulate <i>Escherichia coli</i> (<i>E. coli</i>) and ampicillin (Amp) and droplets that co-encapsulate Amp-resistant (AmpR) <i>E. coli</i> with Amp only based on the conductivity-dependent DEP force (<i>F_DEP</i>) without the assistance of optical analyses. The 9.4% low conductivity (LC) Luria–Bertani (LB) broth diluted with 170 mM mannitol can maintain <i>E. coli</i> and AmpR <i>E. coli</i> growth for 3 h and allow Amp to kill almost all <i>E. coli</i>, which can significantly increase the LCLB conductivity by about 100 μS/cm. Therefore, the AmpR <i>E. coli</i>/9.4%LCLB/Amp where no cells are killed and the <i>E. coli</i>/9.4%LCLB/Amp-containing droplets where most of the cells are killed can be sorted based on this conductivity difference at an applied electric field of 2 MHz and 100 V_pp that generates positive <i>F_DEP</i>. Moreover, the sorting ratio significantly decreased to about 50% when the population of AmpR <i>E. coli</i> was equal to or higher than 50% in droplets. The conductivity-dependent DEP-based sorting platform exhibits promising potential to probe the ratio of AmpR <i>E. coli</i> in an unknown bacterial sample by using the sorting ratio as an index.