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Abstract Long COVID is a multi-systemic disease characterized by the persistence or occurrence of many symptoms that in many cases affect the pulmonary system. These, in turn, may deteriorate the patient’s quality of life making it easier to develop severe complications. Being able to predict this syndrome is therefore important as this enables early treatment. In this work, we investigated three machine learning approaches that use clinical data collected at the time of hospitalization to this goal. The first works with all the descriptors feeding a traditional shallow learner, the second exploits the benefits of an ensemble of classifiers, and the third is driven by the intrinsic multimodality of the data so that different models learn complementary information. The experiments on a new cohort of data from 152 patients show that it is possible to predict pulmonary Long Covid sequelae with an accuracy of up to $$94\%$$ 94 % . As a further contribution, this work also publicly discloses the related data repository to foster research in this field.