Sustainability is a common concern in intermodal transport. Collaboration among carriers may help in reducing emissions. In this context, this work establishes a collaborative planning model for intermodal transport and uses eco-labels (a series of different levels of emission ranges) to reflect shippers’ sustainability preferences. A mathematical model and an Adaptive Large Neighborhood Search heuristic are proposed for intermodal transport planning of carriers and fuzzy set theory is used to model the preferences towards eco-labels. For multiple carriers, centralized, auction-based collaborative, and non-collaborative planning approaches are proposed and compared. Real data from barge, train and truck carriers in the European Rhine-Alpine corridor is used for extensive experiments where both unimodal carrier collaboration and intermodal carrier collaboration are analyzed. Compared with non-collaborative planning without eco-labels, the number of served requests increases and emissions decrease significantly in the collaborative planning with eco-labels as transport capacity is better utilized.