Background: Health technology assessment (HTA) bodies across Europe rely on explicit factors for decision making. However, additional undefined factors play a role. This mixed-methods research aimed to identify the implicit factors involved in HTA deliberative processes in five European countries, and to analyze their impact on decision making. Methods: Between February and May 2021, semi-structured interviews (n = 20) were conducted with HTA experts of three different profiles (chair, advisor, and committee member) from France, Germany, Italy, Spain, and the United Kingdom. The degree of influence of a set of implicit factors and attributes that play a role in the HTA deliberative process, as previously identified in a systematic literature review, was scored by the experts. Experts were also asked to make recommendations on ways of improving the deliberative process. A qualitative analysis and descriptive statistics of quantitative variables are reported. Results: Most (18/20) experts concurred that implicit factors play a role in the HTA deliberative process. Recommendations for improving the process fell into three categories: transparency, methodology improvement, and stakeholder involvement. The results suggest a need for 1) increased external involvement HTA and 2) development of a methodology to mitigate the influence of implicit factors in the deliberative process. This could be achieved by updating the current frameworks to acknowledge these implicit factors and by developing methods to address them.