In the Mediterranean area, using organic fertilizers is crucial to maintaining and increasing soil fertility and crop productivity since soil organic matter is being progressively depleted due to climate change effects. Therefore, the aim of this study was to compare two different organic fertilizers (MC1 without and MC2 with an inoculum of selected microorganisms), applied at 100% and 50% doses, with mineral fertilization and an unfertilized control: (i) by assessing the agronomic performance of fennel crop; and (ii) by investigating environmental and economic sustainability, through GHG emissions determination, carbon efficiency, and cost analysis. The results of the MC2 were comparable to the mineral fertilization for crop growing parameters (plants and roots dry weights) and marketable yield, irrespective of the amount applied (50–100%), likely due to the inoculum of selected microorganisms. These may have favored the soil microbial activity, the nutrient availability, and better synchronization of N mineralization with fennel N demand with respect to MC1 (with a higher C/N ratio). The MC2 also achieved lower costs than the other treatments. The highest GHG emission value was found in the mineral fertilization treatment, while the lowest was recorded in the unfertilized control treatment. The two organic treatments at 100% were the most carbon-efficient systems because of the highest carbon stocks/output, considering the difference between C stocked/output and the C loss/input emitted.