The market for organic products is growing rapidly, probably attributable to the general customer perception that they are healthier foods, with a better nutritional profile than conventional ones. Despite this, the available studies show limited differences in the nutrient profile of organically and conventionally primary food products. Apart from this literature, no studies have focused on the nutrition profile of commercially prepacked foods. Thus, the aim of the present survey was to compare the nutritional quality intended as nutrition facts of organic and conventional prepacked foods sold in Italy. A total of 569 pairs of prepacked products (organic and their conventional counterparts) were selected from nine food categories sold by online retailers. By comparing organic and conventional products in the “pasta, rice and other cereals” category, the former were lower in energy, protein, and higher in saturates compared to the latter. Organic “jams, chocolate spreads and honey” products were lower in energy, carbohydrates, sugars and higher in protein than their regular counterparts. No differences were found for energy, macronutrients and salt for other categories. Therefore, based on the mandatory information printed on their packaging, prepacked organic products are not of a superior nutritional quality than conventional ones, with just a few exceptions. Consequently, the present study suggests that organic certification cannot be considered an indication of better overall nutritional quality. Further studies examining the nutritional quality of organic foods, taking into account the ingredients used, might better explain the results obtained.