Onions are an important vegetable crop in Serra Gaúcha. However, adequate soil, nutrition, and disease management depend on harvest production and quality. Thus, using organic products as an alternative to conventional management methods has grown recently. This study aimed to evaluate the effect of different soil and phytosanitary management of organic origin on onion productivity. Three soil management methods were tested: soil without vegetation cover, soil with vegetation cover, and soil with vegetation cover plus Bokashi compost. The subplots corresponded to the weekly application of ginger extract, biweekly application of Bordeaux mixture, and control (water) for phytosanitary treatments. None of the phytosanitary treatments had any effect on the crop. Soil management influenced the severity of leet rust (Puccinia porri), where the use of straw and the concurrent application of straw and Bokashi reduced the severity. Straw and straw associated with Bokashi, although it produced plants with lower height and stem diameter, promoted greater bulb masses and productivity and increased soil fertility. Thus, the concomitant use of straw and Bokashi can be a strategy to increase onion productivity, which aligns with the principles of organic agriculture.