Abstract Globally, even as environmental protection and sustainability are becoming increasingly important, freight transportation firms are faced with the enormous need to reduce the significant environmental burdens that accrue from transport vehicles. Eco-innovation can aid freight transport firms through fostering sustainable transportation alternatives at best possible costs to ensure effective decision- making for freight logistics sustainability. Yet, freight logistics companies are faced with numerous difficulties when attempting to implement eco-innovation practices along their supply chains. This paper therefore identifies the challenges to implementing eco-innovation practices for freight logistics sustainability to aid management to take informed decisions to overcome these challenges before the environmental burdens become critical. The Best- Worst method is adopted to evaluate and rank these challenges in terms of their relative importance in Nigeria, an emerging economy, which is characterized by increased consumption due to huge population size coupled with government green requirements. The results depict that unavailable funds, lack of clarity on the financial benefits of eco-innovation practices, poor technology infrastructure and reluctant attitude towards eco-innovation practices are the most pressing challenges amongst the challenges faced by Nigeria freight logistics companies. These results will provide insight and guidelines for decision-makers and policymakers in the freight logistics sector who seeks to integrate eco-innovation initiatives to achieve sustainability.