This study aimed to compare agricultural practices, soil physical and chemical properties, growth characteristics, and nutrient uptake of bulb onions from organic and conventional farms in southeastern Korea during the 2011–12 growing season. Soil and plant samples were collected from eight certified organic fields managed organically for more than 5 years and eight conventional fields adjacent to the organic fields. The amounts of nutrients applied to onion fields were approximately two times greater with the conventional methods than with organic methods. However, the soil physical and chemical properties were not significantly different between the organic and conventional systems, except for NO3-N in early May. Growth characteristics were significantly different in early April with organic bulb yield of 55.9 t·ha−1, which was 21.8% lower than conventionally produced onions. Yield reduction in organic onions was the result of lower large-sized (8 cm or greater) bulb yield compared with conventional production. In the conventional system, phosphorus (P) and potassium (K) content of leaf tissue in early April, and nitrogen (N) and P content of bulb tissue in early May were higher than those in the organic system. Uptake of all nutrients was greater in the conventional onions compared with the organic onions, except for leaf tissue at harvest. In conclusion, organic onions began to grow and absorb soil nutrients later than the conventional onions in the initial vegetative growth stage. Moreover, it led to an organic onion producing a lower bulb yield. To accelerate the initial growth of the organic onion plant, agricultural practices need to be modified. Modifications that may help include using larger sized seedlings at transplanting, covering the plants with nonwoven fabric or transparent plastic film to increase warmth during winter, and harvesting the onions 1 week later than the conventional onions.