In recent years, integrating sustainability into the freight transportation (FT) system is progressively gaining global attention. The adoption of sustainability best practices acts as a critical link between the integration process and the sustainable performance of freight transporters. The principal objective of this study is, therefore, to propose a list of best sustainability practices relevant to the FT system. This study considers India a suitable context for the research as environmental emissions due to FT in India are substantially increasing with the upsurge in freight demand. It is, therefore, imperative to embed sustainability values within the freight operations to minimize the environmental and societal implications of freight movements. This study identifies twenty-four sustainability best practices through an extensive literature review, which are clustered into four main categories, namely (a) organizational, (b) process-oriented, (c) technological, and (d) collaborative sustainability practices. These practices are further quantified and prioritized using an integrated approach that innovatively combines intuitionistic fuzzy numbers with the graph theoretic and matrix approach. The quantification and prioritization processes were carried out using expert opinions collected through focus group sessions. Unlike conventional perception, the results of the study show that top management commitment, multi-modal freight transportation, and adoption of green technologies have a higher share of impact on the overall performance of the freight organization. The proposed study is one of the few works, which may act as a guideline for managers and decision-makers seeking to integrate sustainability into freight operations. From the perspective of methodological contribution, this is the first study in the freight transportation literature that has integrated intuitionistic fuzzy numbers with graph-theoretic and matrix approach. One of the uniqueness of the proposed integrated model is that it evaluates both the negative and positive influences of sustainability practices on the freight transporter's economic, environmental, social, operational, and technological performance. © 2022 Elsevier Ltd