Zoledronic acid (ZA), the third-generation nitrogen-containing bisphosphonate, is one of the most effective bisphosphonates and is used as a highly potent inhibitor of bone resorption with no adverse effects on bone mineralization. It is also used to treat multiple cancers, such as lung cancer, bone cancer, breast cancer, and prostate cancer. A microfluidic system can generate an adjustable flow rate and pressure inside multiple channels with the desired shape and dimensions, which are often fabricated from PDMS polymer. Among the advantages of these systems are precise control of environmental conditions, reduction of user intervention, and reduced time and reagent volumes. The microfluidic method, as a simple and cost-effective process with high capability, leads to particle size control, narrow size distribution, and the spherical shape of nanoparticles. With the rapid development of microfluidic technology, the preparation of particles with controlled size, morphology, and composition would be possible with this approach. In this study, to the best of our knowledge, the evaluation of the cytotoxic activity of microfluidic synthesized chitosan-zoledronic acid (CS-ZA) nanoparticles has been investigated for the first time in order to develop new cancer therapy strategies by using pharmaceutical nanotechnology. A microfluidic synthesis of nanoparticles with a narrow size distribution and uniform morphology through the ionic gelation of chitosan (CS) with ZA without a crosslinker was explained in detail in the previous article (Khayati et al., Int J Biol Macromol 234, 2023). This study aimed to evaluate the cytotoxic effect of the best microfluidic synthesized nanoparticles with ZA solution as core flow, CS as sheath flow, and flow ratios of ZA/CS = 0.5 (denoted by MFCSZA0.5) along with synthesized bulk nanoparticles (BCSZA) on the A549 lung cancer cell line through an MTT cell viability assay and a flow cytometric apoptosis assay. The results indicate that MFCSZA0.5 demonstrated significantly greater antitumor activity compared to BCSZA and free ZA. The in vitro drug release from MFCSZA0.5 microfluidic synthesized nanoparticles depicted a gradual, sustained release profile compared to BCSZA synthesized in bulk conditions. However, both of these nanoparticles exhibit promising carriers for intracellular delivery of ZA molecules, which ultimately affect cancer cell viability. The microfluidic method demonstrated a high drug entrapment efficiency compared to the bulk method, and it showed a more controlled in-vitro release of the drug. The synthesized nanoparticles in both microfluidic and bulk methods were found to have an anticancer effect comparable to the free ZA drug.