The use of complementary and alternative medicine (CAM) has been widely recognized as a potential contributor to the emergence of vaccine scepticism and refusal. However, a direct correlation between trust in CAM and vaccine scepticism is still a matter of discussion. The objective of this study is to explore the multidimensional factors that explain the association between CAM usage and vaccine scepticism. Qualitative and quantitative research designs were adopted to examine whether visiting CAM practitioners directly contributes to vaccine scepticism and to identify whether antivaccination attitudes are caused by other social, and cultural factors. These findings support the idea that CAM users tend to exhibit more vaccine scepticism compared to non-users. However, preferring a holistic health model, individual autonomy, and a negative perception of biomedicine representatives emerged as more influential factors in understanding the connection between the prevalence of CAM utilization and vaccine scepticism. Taken together, these results suggest that CAM itself is not the direct predictor of vaccine scepticism. To build trust between the population and vaccines, this information can be used to develop targeted interventions aimed at strategies to improve healthcare services and develop the soft skills of medical doctors.