Your edible garden needs to be cleaned up much more thoroughly in the fall than the perennial gardens
A vegetable garden is much more susceptible to disease and pests than a perennial garden. Virtually every year at least some of your edible plants are harboring blight, fungus, mildew or worse. So it is critical that you properly clean out the vegetable beds at the end of each season.
There are many advantages to clearing out your vegetable gardens, even though you should leave some plants stand in your perennial gardens.
Seed from fallen fruits will seed next season.
Fallen fruits will rot and invite pests and disease.
Diseased plant matter will allow the affliction to remain in your garden next season or spread into the soil
Pest infested plant matter will harbor eggs, larvae or adults over winter to proliferate next season.
Weeds can be eliminated before the spread.
A cover crop can be planted on the cleared bed to benefit the soil in many ways.
At minimum, the cleared beds can be covered with shredded leaves or straw (NEVER hay, which is full of weed seeds) that will hold and feed the soil. It can all be turned into the soil next spring or plant with it in place. However, if you had squash bugs this season you may want to keep that area clear. The adults will overwinter under leaves and mulch.
Other than perennial produce of course, there are just a few plants that do not need to be completely removed:
The roots of peas and beans can be left behind. They are nitrogen fixers and garden microorganisms will feed off them all winter.
Borage leaves are loaded with trace minerals and many gardeners dig them right into the soil in fall. At the least they should go in the compost heap.
I don’t worry about removing my herbs as they are not generally afflicted with disease or pest. These few plants can provide a little habitat for beneficial insects.
Any healthy plants can be added to your compost, all diseased plant material should be disposed of with lawn refuse or burned so disease is not added back to your gardens with the compost.