Background: The rise in unprecedented pressure of producing enough food for an ever-growing human population resulted in the use of considerable amounts of agrochemicals in crop production. To overcome this, inclusion of annual pulse crops such as cluster beans (Cyamopsis tetragonoloba L.) in cropping systems is an alternative technique for enhancing output while minimising environmental impact. Therefore, to assess the influence of different crop production systems on yield, quality and soil fertility attributes of fennel (Foeniculum vulgare L.)-cluster bean (Cyamopsis tetragonoloba L.) crop sequence, a long term field experiment was conducted. Methods: A field experiment was conducted on fennel (Foeniculum vulgare L.) cluster bean (Cyamopsis tetragonoloba L.) crop sequence under AI-NPOF Project during 2016-17 to 2020-21 at ICAR-National Research Centre on Seed Spices, Ajmer (Rajasthan), India. The experiment was laid out as a factorial design based on randomized complete blocks (RCBD) with three replications. The first factor consisted of six production systems viz., (PS1) - 100% organic, (PS2) - 75% organic + 25% innovative practice (Compost extract, cattle urine), (PS3) - Integrated (50% organic + 50% inorganic), (PS4) - Integrated (75% organic + 25% inorganic), (PS5) -100% inorganic nutrient sources and (PS6) - State recommendation] including fennel (Rabi season) - cluster bean (Kharif season) cropping sequence, whereas the second factor included the environment over the period. Result: The outcomes of study revealed that production system (PS4) - Integrated (75% organic + 25% inorganic) resulted in the maximum seed yields and yield attributes of cluster bean (1501.87 kg ha-1) and fennel (1970.19 kg ha-1). The study shows that the production system (PS4) had a 17.29 and 30.75% increment of protein as compared to PS5 and PS1 in fennel and cluster beans, respectively. Under production system PS1, the per cent increment of soil organic carbon (~25.2%) and readily available N (~9%), P (~38.5%) and K (~Non-significant) were noted over the years respectively, compared with production system (PS5). A significant positive association was observed between fennel and cluster bean grain yield and soil organic carbon (P less than 0.01) and the Shannon-Wiener indexes (R2 = 0.75, R2 = 0.69), respectively. The combined assessment of yield, quality, soil organic carbon and soil sustainability shows that rotations based on legume crops performed better and provided a model of sustainable crop intensification. Thus, adding legume to the cropping system and implementing integrated nutrient management (INM) could gradually improve soil quality in agro-ecologies where fennel predominates.