Woody plants serve as habitats for a diverse range of organisms, including herbivores and pathogenic species, which are often considered to be both harmful and beneficial organisms that support plant health and ecosystem stability. For instance, natural enemies of pests are essential for preserving the health of wild woody plants, managed forests, and ornamental trees in urban green spaces such as parks, gardens, and urban forests. While the interactions between woody plants and herbivores have been well documented, much less is understood about the complex relationships among the various organisms that inhabit these plants. In this Special Issue, the different contributions by the authors provide critical insights into the multifaceted roles of invertebrates and microorganisms in diverse ecosystems, significantly enhancing our understanding of ecological dynamics and pest management. As such, this Special Issue offers valuable examples of recent research activities in this global discipline.