Diversification of conventional food-based cropping system with multipurpose lignocellulosic crops could increase biodiversity, farmer’s market opportunities, feedstock for biorefineries, though can also imply soil organic carbon (SOC) stock changes, without competing with food production. Sunnhemp ( Crotalaria juncea L.), biomass sorghum ( Sorghum bicolor L.), kenaf ( Hibiscus cannabinus L.), and industrial hemp ( Cannabis sativa L.) are annual high yielding lignocellulosic crops with great potential for their multiple applications. The objective of the present study was to identify the SOC changes when the aforementioned crops are grown during the fallow periods of a conventional maize ( Zea mays L.)-wheat ( Triticum aestivum L.) rotation over five years. For this purpose, the SOC, carbon inputs (i.e. above and belowground residues), soil respiration , and cumulative CO 2 emissions were evaluated. The experiment was carried out in northern Italy (44°30′ N, 11°21′ E) from 2016 to 2021 in a randomized complete block design (n = 4) by adopting conventional field and harvest management practices (i.e. straw removal with hay machineries and alternating conventional with minimum tillage). The SOC stock increased by 7% from 2016 (56 Mg ha −1 ) to 2021 (60 Mg ha −1 ), regardless of the rotation system. Despite one of the highest CO 2 cumulative soil emissions (11 Mg ha −1 , two and three times higher than sunnhemp, kenaf, and industrial hemp, respectively) the rotation including biomass sorghum ended with higher SOC concentration (7.6 g kg −1 ) compared with industrial hemp (7 g kg −1 ) and kenaf (6.9 g kg −1 ), whereas fallow (7.2 g kg −1 ) and sunnhemp (7.1 g kg −1 ) showed intermediate values. The combination of high aboveground residues and high nitrogen fertilizations are deemed to act primarily on SOC level compared with belowground residues. In summary, the crop intensification did not deplete SOC, moreover biomass sorghum cropping system outperformed kenaf and industrial hemp through the decomposition into SOC of higher released residues. The rotation including sunnhemp coupled high SOC levels with low CO 2 emissions, raising interest in the light of its nitrogen fixing ability which can further help reducing the system’s carbon footprint. • Cropping systems with wheat and maize including lignocellulosic crops during the fallow period are presented. • Over five years, the SOC carbon stock increased by 7%, regardless of rotation. • The rotation resulting with the highest SOC concentration included biomass sorghum (7.6 g kg −1 ). • The rotation resulting with the lowest SOC concentration included industrial hemp (7 g kg −1 ), and kenaf (6.9 g kg −1 ). • Aboveground crop residues, reduced tillage and nitrogen fertilization are likely the main drivers influencing SOC.