The most common tall trees in Madrona Woods are big-leaf maples. Other deciduous trees here are beaked hazelnut, red alder, red elderberry, western dogwood, Oregon ash and black cottonwood. The tallest evergreen trees are the conifers—Douglas-firs, western red cedars and western hemlocks—which have needles and cones. The Pacific madrone is a native evergreen that is not a conifer. Much of the understory in the Woods is still filled with holly and laurel, but you can find many native shrubs that have been uncovered or planted. These include salal, Oregon grape, snowberry, Oregon viburnum, red and evergreen huckleberry, red flowering currant, oceanspray, wood sorrell and Indian plum or osoberry. The Himalayan blackberries that have taken over in places are an invasive species, but native berries include thimbleberry and salmonberry.

Several kinds of ferns grow in the Woods, but the most common is the sword fern. You can also find lady ferns and bracken ferns and licorice ferns growing in the maple trees. A few deer and maidenhair ferns have been planted. Native plants sharing the forest floor with the ferns at different seasons of the year include wood sorrel, horsetail (equisetum), stinging nettle, skunk cabbage, trillium, cow parsnip, bleeding heart, columbine, climbing honeysuckle, clover, fringe cup, inside-out plant, vanilla leaf, wild ginger and violet.