There is little information about the potential effects of compost and zeolite or zeolite with leonardite as soil amendments in barley cultivation. Thus in this study, the following objectives were proposed: i) to compare the effects of the addition of compost, alone or simultaneously with zeolite, and of the addition of leonarditeenriched zeolite with those of the conventional NPK fertilization used in barley cultivation, on the soil nutritional status, microbial community structure, and enzyme activity in different stages of barley cultivation; and ii) to establish relationships between the different soil parameter trends, soil microbial community structure, and barley crop yield. In the field experiment carried out with a barley crop, the alternative fertilization treatments tested had an overall positive effect, in comparison with conventional fertilization with a mineral NPK fertilizer, when soil quality parameters, the nutritional level and yield of the barley crop were analyzed. Zeolite with leonardite increased barley yield in comparison with the compost treatments, either with zeolite or without, but had an excessive contribution to the water soluble contents of Na and N in soil. So, using environmental and agronomic criteria, the most rational action would be the use of compost in agriculture.