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Acceptance and willingness to receive the vaccine are among the main factors in the success or failure of a health system in implementing the vaccination program. The present study was conducted in Tehran, the political and economic capital of Iran, to determine the acceptance of the COVID-19 vaccine and identify its associated factors, and explain the most important barriers and acceptance strategies for vaccination. This research was a concurrent quantitative and qualitative mixed-method study. In the quantitative part, 1200 individuals aged more than 18 years were selected from the households in 22 districts of Tehran City, with a multistage stratified cluster sampling method. Two questionnaires were used to evaluate the acceptance of the COVID-19 vaccine and vaccine acceptance determinants. The qualitative content analysis method addressed the influencing factors, as well as challenges and strategies related to the acceptance of the COVID-19 vaccine in four groups of Tehran inhabitants: the elderly, people with underlying diseases, healthcare workers, and the general population. The related data were simultaneously collected by applying in-depth semi-structural interviews and a data analysis process. Furthermore, we used the Graneheim and Lundman method for data analysis. We analyzed the data of 1200 people with a mean (SD) age of 46.4 (11.1) years, and approximately 58% of them were men. The vaccine acceptance was 83.6% (95% CI: 81.3–85.9). Among those who welcomed vaccination, 58% preferred the imported vaccines, 25% the Iranian ones, and 17% both. There was a significant association between the variables of age (adjusted odds ratio [AOR] = 1.72, 95% CI: 1.01–2.93), being single (AOR = 0.54, 95% CI: 0.41–0.91), moderate pharmacotherapy adherence (AOR = 0.58, 95% CI: 0.4–0.85), and the willingness to receive COVID-19 vaccine. Qualitative study after interviewing 45 people from four study groups showed an insufficient social trust in healthcare system officials, pharmaceutical and vaccine production companies; distrust in the effectiveness of the vaccines, concerns about the vaccine adverse effects, being tracked by microchips after vaccination, traditional anti-vaccination movements, the feeling the inessentiality of vaccination, and uncertainty about the fair distribution of the vaccine. These concerns were the main challenges addressed by the study groups. A good proportion of Tehran residents reported their willingness to receive the COVID-19 vaccine. Additionally, they expressed their critical concerns, such as insufficient trust in the healthcare system, vaccine safeties, and adverse effects that were the significant barriers to vaccine acceptance. It seems that conflicts raised by the shortage of vaccines and their import due to the sanctions have led to intense desire and demand in the general population, and especially the elderly, for vaccination. Besides, vaccination phobia in some individuals requires further investigations.