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Inulin is accumulated as a reserve carbohydrate in the roots and tubers of many plants belonging to the Asteraceae family. At present, most of the inulin for nutraceutical purposes is produced from Jerusalem artichoke (Helianthus tuberosus L.) and Chicory (Cichorium intybus L.), and cardoon is proved to synthetize and store a high quantity of inulin in roots. Inulin in the roots of cardoon reaches the maximum content before the beginning of flowers formation in May. Due to the limited favorable period for harvesting the roots, storage plays a key role in the supply chain. The complete drying of cardoon roots before the storage has been proved to prevent the degradation of inulin up to 6 months of storage. Because drying is a costly operation, in the present study, energy-saving and the effect on percentage inulin content in cardoon roots dried at different moisture contents before storage were assessed. From 48.2% inulin retrievable at the beginning of the investigated period (100% dry matter), after 1 month of storage, about 2% reduction was recorded on average in H0 and H12.5 treatments, while about 10% reduction was shown (with no statistical differences) in treatments at higher moisture contents (TQ, H50, and H25). These values remained constant until the end of storage, except for TQ treatment, where inulin content decreased progressively up to 38.7% w/w. From an economic point of view, limiting the drying time and storing roots at a moisture content higher than 0% leads to an income loss of 2,000–3,000 €/t of roots. Therefore, full drying is the most cost-effective solution in the optic of producing the highest possible amount of inulin and could be avoided just in the case of immediate roots extraction and processing in a few days.