Vaccination to prevent coronavirus disease 2019 (COVID-19) emerged as a promising measure to overcome the negative consequences of the pandemic. Since university students could be considered a knowledgeable group, this study aimed to evaluate COVID-19 vaccine acceptance among this group in Jordan. Additionally, we aimed to examine the association between vaccine conspiracy beliefs and vaccine hesitancy. We used an online survey conducted in January 2021 with a chain-referral sampling approach. Conspiracy beliefs were evaluated using the validated Vaccine Conspiracy Belief Scale (VCBS), with higher scores implying embrace of conspiracies. A total of 1106 respondents completed the survey with female predominance ( = 802, 72.5%). The intention to get COVID-19 vaccines was low: 34.9% (yes) compared to 39.6% (no) and 25.5% (maybe). Higher rates of COVID-19 vaccine acceptance were seen among males (42.1%) and students at Health Schools (43.5%). A Low rate of influenza vaccine acceptance was seen as well (28.8%), in addition to 18.6% of respondents being anti-vaccination altogether. A significantly higher VCBS score was correlated with reluctance to get the vaccine ( < 0.001). Dependence on social media platforms was significantly associated with lower intention to get COVID-19 vaccines (19.8%) compared to dependence on medical doctors, scientists, and scientific journals (47.2%, < 0.001). The results of this study showed the high prevalence of COVID-19 vaccine hesitancy and its association with conspiracy beliefs among university students in Jordan. The implementation of targeted actions to increase the awareness of such a group is highly recommended. This includes educational programs to dismantle vaccine conspiracy beliefs and awareness campaigns to build recognition of the safety and efficacy of COVID-19 vaccines.