Organic amendments are important sources of nutrients that release upon organic matter degradation, yet the stability of these organics in arid and semi-arid regions is relatively low. In contrast, humic substances (HS) are resistant to biodegradation and can keep nutrients in the soil available for the plant over a long time. Combinations between humic substances (HS) and mineral-N fertilizers are assumed to retain higher available nutrients in soils than those recorded for the sole application of either mineral or organic applications. We anticipate, however, that humic substances might not be as efficient as the organics from which they were extracted in increasing NP uptake by plants. To test these assumptions, faba bean was planted in a pot experiment under greenhouse conditions following a complete randomized design while considering three factors: two soils (calcareous and non-calcareous, Factor A), two organics (biogas and compost, Factor B) and combinations of the organics and their extracts (HA or FA) together with complementary doses of mineral-N ((NH4)2SO4) to attain a total rate of 50 kg N ha−1 (the recommended dose for faba bean plants) (Factor C). Results indicated that nitrogenase activity increased significantly due to the application of the used organics. In this respect, compost manure caused higher nitrogenase activity than biogas manure did. Humic substances raised NP-availability and the uptake by plants significantly; however, the values of increase were lower than those that occurred due to the compost or biogas manure. Moreover, the sole application of the used organics recorded the highest increases in plant biomass. Significant correlations were also detected between NP-availability, uptake and plant biomass. This means that HS could probably retain nutrients in available forms for long time periods, yet nutrients released continuously but slowly upon decomposition of organics seemed more important for plant nutrition.