Is it better to clean flowerbeds in the fall, or wait until spring? There are advantages and disadvantages of both. After a few frosty nights, you should remove annuals and cut back tops of some tall herbaceous perennials. Flowers and vegetables whose foliage has begun to brown and shrivel due to frost could be removed before winter. Removing the spent foliage reduces the chance for fungi and insect pests to over winter. Peonies often get a fungal disease called grey mold or botrytis blight. Once peony plants are infected with this disease, it is difficult to cure them.  This fungal disease can survive on dead vegetation, the vegetation’s removal in the fall should be a priority. Garden phlox and monarda are frequently troubled with powdery mildew. The spores of this disease also thrive in dead vegetation.  The surviving spores on dead foliage will then serve as an inoculum the following season resulting in re-infestation. Peony, monarda, and phlox should be cut back to just above the crown of the plant, the place where the stems join the roots. Do this in fall to reduce disease problems next year. Annual plants should be completely removed from the garden in fall. Healthy plant refuse can be composted to recycle into organic matter to add to the garden soil next year. Some plants, such as ornamental grasses, provide winter interest in their dried state. These plants can be left until later winter or early spring. Cut back the dead stems before the new foliage comes up. You can wait to clean up the lilies until they are killed by frost.Cut off the spent lily flowers, but leave the stem and leaves until it dies back. Then cut it off at the soil surface. After the soil surface freezes in late fall, mulch the soil with shredded tree leaves. The biggest disadvantage of fall cleanup is exposing the crowns of sensitive perennials to winter weather. Standing dead vegetation captures leaves and snow. This accumulation of debris insulates the soil and protects vulnerable dormant perennials from our freeze/thaw cycle.

The following is a new invasive insect that eats lily leaves. Please look for it when you clean up your lilies.

https://extension.umn.edu/yard-and-garden-news/invasive-lily-leaf-beetle-found-minnesota

These site give more details.

https://extension.unl.edu/statewide/buffalo/Fall%20vs.%20Spring%20Garden%20Cleanup%2011-16-2013%20%283%29.pdf

https://extension.illinois.edu/blogs/garden-scoop/2017-11-08-fall-garden-cleanup-and-wildlife