I have found that it can be a great challenge to maintain organization in a frequently-used, well-stocked pantry. It does help to be diligent when those groceries come in the door. No haphazard throwing of the items on the shelves! Take an afternoon to assess your space, your cooking/snacking habits, and deliberately arrange the items in a way that suits your family. If the toddler has access to the pantry, avoid placing breakables, candies and goodies, and other such non-kid-friendly items near the floor. Consider, rather, paper goods, linens, or the like.
Baskets are wonderful tools for pantry spaces! They can help corral anything from plastic utensils to dried peppers, canned goods to loaves of bread, etc. I am also currently using cardboard boxes (unprinted-side facing out) and brown paper bags to hold entire categories of food. It is working very nicely!