Background: The electronic Freight Transport Information (eFTI) regulation is critical in modernizing freight transport (FT) within the European Union by establishing a framework for the electronic exchange of information. Despite its importance, there is a notable gap in the literature regarding the practical implementation challenges, especially from an empirical perspective. Methods: To address this gap, our study utilized a grounded theory approach, conducting interviews with a diverse group of logistics experts from Greece. The selection of experts was strategic to ensure a comprehensive range of knowledge and expertise, including insights at the policy level as well as practical experiences. Results: Our findings highlight several significant challenges in the implementation of eFTI, including the digital skill gap among the workforce, issues with system interoperability, and diverse capacities and resources of companies of different sizes. Economic factors, regulatory frameworks and the necessity for targeted training and leadership support were also identified as crucial for the digital transition. Conclusions: The study shows that uniform eFTI implementation may not work for all organizations, highlighting the necessity for customized strategies that address specific challenges in the FT chain. Our research deepens the understanding of these issues, providing actionable insights for successful eFTI adoption.