The refrigerator is truly the home, from-scratch cook's best friend. Here you can store most of the fresh, whole, close to the source ingredients you will need to have on hand for your meals.
A word of warning: refrigerators can become the black hole of ingredients - try to organize yours so that ingredients get rotated regularly, meaning the oldest get used first. Resist the urge to put things in front of containers that are already in there - take the time to put new acquisitions behind the old ones, or you will be destined to throw away a lot of food.
Organize the fridge well, and your life will be much easier: keep dairy products in one section, "basics" in another, fruits and vegetables in bins with the correct humidity setting, leftovers all on one shelf, etc.
basics
The building blocks of from-scratch cooking should be stored in stackable containers that are see-through or well-labeled: cooked rice, beans, pasta, and cleaned/cut veggies all make quick weeknight meals a snap.
condiments, pickles, and relishes
The door shelves are a great place for these items, keeping them in plain sight and preventing them from getting shoved to the rear and being lost for eternity.
dairy
Eggs, milk, butter, yogurt and cheese: the coldest part of the fridge is usually the best for these items.
deli
One of the few processed foods we do buy are deli meats - I always look for the organic, sustainably raised varieties - which are a parent's best friend for quick school lunches. Most sliced meats of this type should be stored in the coldest part of the fridge (usually near the bottom, toward the back) and eaten within a few days of opening.
fruit
Most of our fruit lives in bowls on the countertop, but grapes, ripe stone fruits and melons, berries, and citrus do well in the refrigerator for a brief time - try to eat them within 48 hours of refrigeration.
leftovers
We keep a large amount of containers on hand for leftovers, which get consumed for weekday lunches - be sure to invest in stackable containers with tight-fitting lids, and if you use plastic ones, transfer the food to a glass or other microwave-safe plate before microwaving. Glass containers are great because they can go from oven to fridge and back again. Be sure to rotate your leftovers - first in, first out is a good rule to follow, and if something just doesn't get eaten within a week, it's probably not going to be eaten!
meat/fish/poultry
Having switched to buying pastured meat and poultry and sustainably farmed or wild caught fish, I keep the bulk of my animal proteins in the freezer, removing what I need for the next day or two in advance and thawing it in the refrigerator. Small cuts normally thaw within 24 hours, larger roasts and whole chicken in 48 hours. The thawing should happen in the cooler part of the fridge, usually toward the bottom and the back. Food safety note: be sure that you prevent raw meat juices from dripping onto foods that will be consumed raw - the simplest way to do this is place the thawing items on a place or in a bowl in case the packaging is not what it should have been in the first place.
vegetables
Onions, carrots, celery, broccoli, cauliflower, cabbage, spinach, greens, beets.... Just about all vegetables do better in the refrigerator than at room temperature, the notable exceptions being tomatoes. If you're lucky to have a large refrigerator with several adjustable bins, set one to a higher humidity level for the leafies, one for lower humidity for the roots and fruits.
yeast
If you are only an occasional baker of yeast products, keep your yeast in the refrigerator to extend its shelf life.

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