There are several costs involved in gaining organic certification. Not only is there an annual fee, but some farms may have to hire additional employees to assist in daily record-keeping or make modifications to their land and equipment in order to comply.
Conventional farms use chemical fertilizers that are cheap to purchase and ship. By contrast, organic farmers fertilize with manure or compost — if they can't produce enough organic fertilizer on their own farm then they can purchase more, but these types of fertilizers are expensive and cost more to ship than their synthetic counterparts.
Choosing to control weeds without chemicals also means that organic farmers must practice crop rotation and cover-cropping to maintain soil health and discourage the growth of weeds. Simply put, organic farmers rotate the crop they're growing on a particular plot of land (even if that means growing less profitable crops at certain points throughout the year) so that the soil will have the nutrients it needs to prevent weeds from growing. By contrast, non-organic farms can grow the most profitable crops year-round, which further reduces the costs of growing conventional produce.
Organic products also refrain from the use of growth enhancers and hormones. This means crops and animals can take longer to reach maturity. The extra time spent caring for these plants and animals, and the delay in profit from their sale, raises the cost of organic products further.
Because organic farmers don't use chemicals, they lose more crops and animals to pests and disease than conventional farmers do. They also have to account for the shortened shelf-life of their chemical- and preservative-free products; some products go bad before they're sold.