(Updated 2025)
The last of the warm, dry fall days are upon us and it seems like a great time to be puttering around the garden. But this time of year is actually not a good time to be “cleaning up”— that is, removing fallen leaves and woody debris from bare soil, pruning standing plants, applying heavy mulch, and making your yard look somewhat like a victim of a gardening magazine makeover. Leaves and other plant material that fall to earth are part of nature’s systems that nurture and shelter wildlife, enrich and protect the soil, and offer many other benefits. Healthy soil has an uncanny ability to not only keep plants thriving, but also store carbon.
Bedtime for bugs
Leaving fallen leaves on soil is one of the best (and easiest!) things you can do to support wild ones such as birds, amphibians, and small mammals in your garden, as well as myriad invertebrates, including bees, butterflies, spiders, beetles, and worms. Leaves and other plant matter are meant to fall to the soil, to provide food for unfathomable numbers of microbes as well as the macroscopic consumers and recyclers that feed on decaying plant matter. Further up the food chain, many creatures — ground-feeding birds, for example — rely on nature’s soil cover to provide for those they need to eat, which they find under leaves and downed wood (fallen twigs and branches, etc.).
A fox sparrow finds dinner under leafy cover.
If we zoom in a bit, we might see small organisms, such as syrphid fly larvae depending on plant debris for a sort of blanket to help them through the cold, wet winter. As things warm up in springtime, some kinds of syrphid fly larvae will consume enormous quantities of aphids and leafhoppers that can harm our edible plants. Adult syrphid files (also called “hover flies” or “flower flies”) are important pollinators: Spring through late summer I see quite a variety of them in my garden, probably because I prescribe a healthy dose of fallen leaves on the ground in autumn. But thick layers of wood chips, bark, and other heavy materials can make it difficult — if not impossible — for ground-nesting bees to emerge in springtime. Seventy percent of native bees nest in the ground and heavy mulches can bury them alive. And tilling the soil in areas with ground-nesting insects is another practice to be seriously avoided; tilling also destroys soil microbes.
A leafy layer also encourages other pollinators to make it through the winter. For example, as pollination season shuts down and bumble bee workers (females) and males perish, newly crowned bumble bee queens (technically “gyne,” an impregnated queen who has not yet founded a nest but will establish a whole new generation of bumble bees next year) live on. Queens find refuge by digging a shallow tunnel in loose soil — known as a hibernaculum — that’s often tucked under leaf litter. And, many species of lepidoptera (butterflies and moths) overwinter under fallen leaves as eggs, larvae, pupae, or adults. If we disturb their slumber by blowing or raking them away, they and the ecosystem will suffer. Essentially, the simply need to leave them and their habitat alone if we want them to grace our gardens and wilder spaces next year.
Western tiger swallowtail pupa, clinging to wood, waits out the winter and spring.
Don’t cut back
Fall pruning isn’t a good idea because it may stimulate a plant to put on new growth, which could be damaged by the lower winter temperatures soon to come. Another important reason not to prune in autumn is that branches and bark — particularly of native plant species — may support butterfly and moth pupae, (aka chrysalis). Swallowtail butterfly pupae pass the winter attached by thin threads to woody material — disguised as dried up leaves or old bits of wood to fool predators — until the warmer temperatures of spring stimulate their metamorphosis into adults. While some non-native fruit trees do need winter pruning and it’s beneficial to remove diseased and dying annual vegetable garden plants to prevent the spread of disease to next year’s kitchen garden, in all other parts of the yard, if you must prune woody plants, approach it the following spring, being sure not to disturb any nesting birds.
Erigeron speciosus (showy fleabane) seed head. When viewed closely, seed heads can be fascinating in their complexity.
Moreover, although they may look dead, the seed heads of PNW native perennials such as fleabane, fescue, goatsbeard, and lupine provide food for seed-eating birds, while their stems or stalks—pithy or hollow—provide shelter and/or cavity nests for beneficial insects like the wild bees that nest in small tunnels. If you must cut them back to the plants’ bases, do it as late as possible in springtime and, instead of throwing them away, place the cut stems in an out of the way place so that anyone using them to get through the winter won’t be discarded and so that they may be used by the current year’s cavity nesters.
And, aesthetically speaking, allowing fading plants to stand during winter provides structure and form. On cold, frosty mornings they can be magically transformed into silvery jewels.
Protect and nourish the soil
Down at soil level, besides providing a haven for overwintering organisms, fallen leaves and woody debris protect the soil, which can degrade and erode fairly quickly from excessive rain, sunlight, and wind. In nature, soil is protected and mimicking the way it does that will help your soil stay healthy. And over many years, leaves decompose into layers of organic matter that feed plants naturally and gently, improve the condition of soil, and store carbon with the help of mycorrhizal fungi. The other day I relocated a plant to a spot in my front yard that’s been collectively accumulating a couple dozen inches of leaves over the past 15 years. To my delight I found the result of their decomposition: A couple of inches of soft, dark, rich organic matter that wasn’t there a decade ago.
Even when we’re being careful, though, it’s easy to cause disturbance. Many autumns ago, as I moved a small amount of leaf litter to another area, I inadvertently uncovered an overwintering queen bumble bee. I felt terrible as I watched her stumble around, obviously weak and awoken from a sound sleep. Luckily it was a warm, dry day and eventually she flew off into the sunshine. But clearly the awakening had been a rude one, because a short while later she returned and burrowed into some loose soil covered by leaves, just a few feet from where she had been. After she was safely underground, I gingerly placed a couple of particularly interesting rocks several inches from her tunnel’s entrance, as well as some oak leaves on top of the soil to remind myself of where she slept.
Moral of the story: The more we clean up and work towards a neat and tidy garden, the worse off birds, bugs, and countless other life forms will be. If you tend to be a neatnik (like I am), try to catch yourself every time you start moving into manicure-mode and getting overly tidy—especially in the wilder parts of the yard where wildlife may visit or set up house. It just doesn’t make sense to risk losing them for the sake of neatness or to maintain a certain ‘look.’ If you have piles of leaves that have been raked off hardscape or lawn, here are additional ways to use them in your garden.
as an elm. Sharp cuts that don’t leave stubs (partially amputated branches not cut back to the branch collar that look like you could hang a hat on it) will allow for faster healing and may prolong the life of the tree. But if safety is not an issue, consider that natural, important habitat is created when damaged limbs are simply left on the tree. As I wrote in my book, “interactions between wildlife and decaying wood are fundamental to ecosystem functions and processes in forests, aquatic habitats,” 
roughly 15 feet tall and cut back branches. If that’s not possible and you must cut it down, leave the trunk on the ground where it won’t get in your way and leave the stump. If you already have a snag, retain or add native shrubs near its base. They will help keep it protected from weather extremes and provide connectivity, leafy cover, and additional forage for wildlife.
them into your landscape, and the wild ones will thank you.
the quiet beauty that unfolds during all stages of natural decomposition and regeneration. Imagine a “nurse log” in your own yard that will increase biodiversity by providing decades of nutrients and moisture to other plants and soil organisms. While natural, moss-furred nurse logs (fallen forest trunks and limbs) provide complex substrates for regeneration of trees in intact forests, there’s no reason you can’t foster similar function in your yard (but never remove nurse logs from a forest!). Surround a fallen giant with local native ferns and other shade lovers to blend and complement, and the mystery and magic begins. It rots slowly at first, then begins to crumble away, providing more sustenance for other species. After a few decades (or a great deal longer, depending on the species), the log will be reduced to nothing but fragments, but the soil—nurtured, enriched, and full of life—will pass on its riches. Fallen logs hold large amounts of water and nutrients like nitrogen and phosphorus and, with time, concentrate those nutrients to provide even more. And new lifeforms such as bacteria, fungi, protozoa lead to salamanders, beetles and millipedes.
nuthatches, woodpeckers, swallows, or owls that is sited correctly and is accessible for annual cleaning. Though not as good as natural nest sites due to their inability to insulate as real tree cavities do, boxes are better than nothing.