Yes you can. Retail stores are often certified by department, such as produce, meat, bulk foods, prepared foods, etc. Any or all departments can be certified.
If you are certifying a prepared food section – such as a bakery, deli, salad bar, or juice or coffee bar – you may choose to certify only selected items instead of all items. As with all other types of certification where both organic and conventional products are made, you will need to be able to show how you maintain the organic integrity of the ingredients and products by preventing commingling and contamination between organic and conventional products.