Coffee crop management is guided by an approach of synthetic nitrogen fertilizers application in order to guarantee high production rates; however, this type of management increases soil degradation. A study was conducted in order to evaluate the impact of changing soil nutritional management from Chemical (NPK) to Organic (Farmyard Manure-FYM), and from Chemical (NPK) to Mixed (NPK + FYM) regarding soil quality properties and mineral nitrogen available in coffee agroecosystems; a multi-spatial analysis was carried out considering a unifactorial design; soil samples were taken from depths between 0.10 and 0.20 m in 42 plots; physical and chemical variables were measured (ammonium, nitrates, pH, organic matter, moisture, bulk density and texture). It was found that Chemical Management affects the physical and chemical properties of soil quality (organic matter, humidity, bulk density, and pH), resulting in significant differences (p < 0.05) comparing to Mixed and Organic Management. The lowest level of organic matter was found under chemical management, being of 3% and increasing up to 4.41% under mixed management. Mineral nitrogen availability in the form of ammonium, was not affected by nutritional management. A higher concentration of nitrate was found under Mixed Management (105.02 mg NO3 kg−1), presenting significant differences (p < 0.05) against Chemical and Organic. There was no significant difference between Organic and Chemical Management. The study allowed us to determine that, through coffee organic nutritional management, it is possible to keep suitable soil quality conditions in order to reduce soil degradation, and to keep mineral nitrogen available for the development of coffee plants.