Nanoencapsulation of essential oils (EOs) in drug delivery systems leads to their capability of improving their solubility, stability, and bioavailability of them. The aim of this study was preparation, optimization, and characterization of nano-liposomes/nano-niosomes containing Achillea millefolium essential oils (A. millefolium EOs) and comparison of their properties. In the experimental study, characteristics of nanoparticles including size, zeta potential, Fourier Transform Infrared Spectroscopy (FTIR), % encapsulation efficiency (EE%) and the release amount of essential oils from nano-liposome or niosome were assessed using different techniques. Then to determine cell viability at different concentrations, the MTT assay was used. Also, the dilution method was used to determine the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of antimicrobial agents. The optimized formulations provided potential advantages, including an appropriate nano-size scale, and a negative charge, and also showed a continuous drug release behavior, which successfully encapsulated essential oil with high entrapment efficiency. In terms of size and release amount, nano-niosome had superiority to nano-liposome with smaller size and also slower release but nano-liposome could encapsulate essential oils in a higher percentage compared to nano-niosome. Also, there was a significant difference between the toxicity of encapsulated EOs and free EOs in terms of viability (P < 0.05). In addition, the antimicrobial effect of liposomal and niosomal EO was greater than free EO. In conclusion, the designed nano-based systems were determined as promising lipid-based nano-carriers for essential oil delivery that proffered a novel, high potential therapy for breast cancer and favorable antimicrobial effects.