Preheat the oven to 375 degrees. Position an oven rack in the middle of the oven. Have a 9-inch deep dish pie shell ready (thaw if necessary).
Mix the grated cheese and flour in a large bowl. Toss gently so the flour coats the cheese. Set aside.
Add the butter to a small skillet over medium heat. Saute the onion and bell pepper in the butter until the onion is wilted and translucent. Take care not to let the onion brown.
Add the ham, along with the onion and bell pepper mixture to the bowl with the grated cheese. Stir gently but thoroughly. Spread mixture in bottom of the unbaked pie shell. Set the filled pie shell on a rimmed baking sheet.
Combine the remaining ingredients in a medium bowl. Mix thoroughly and pour over the ham-cheese mixture in the pie shell.
Bake for 35-40 minutes or until set.
Notes
Store cooled leftovers tightly wrapped for up to three days in the refrigerator. Reheat individual servings briefly in the microwave.
To freeze, wrap closely with plastic wrap followed by a layer of aluminum foil. Store in the freezer for up to three months.