Conjecture formulation is crucial to mathematics education. Therefore, this study aimed to evaluate challenges prospective mathematics teachers (PMTs) encounter when using GeoGebra to formulate geometrical conjecture. A qualitative case study was conducted with an exploratory strategy to provide a complete comprehension of the occurrence. Six undergraduate mathematics students were selected for geometrical concepts, communication, and willingness. Data collection compromised two phases, including (1) a focus group discussions (FGDs) where participants constructed dynamic geometrical figures using GeoGebra and formulated geometrical propositions based on observations as well as (2) individual interviews to confirm and expand on the results of FGDs. The results obtained through a comprehensive thematic analysis were presented in a coded form. Additionally, the toolset of GeoGebra was new for PMTs, leading to difficulties with distinguishing between the premises and the conclusions, as well as tendencies to formulate conjecture based on knowledge rather than experience. Challenges could be addressed through structured tool tutorials, an incremental approach to learning, instructional modeling, interactive learning activities, scaffolding strategies, enhanced feedback mechanisms, integration into the curriculum, teacher professional development activities, and specially designed learning tasks. This study provided teachers with useful methods of enhancing geometric reasoning and comprehension of mathematical concepts among students when using dynamic geometry software such as GeoGebra.