A current alternative for sustainable development through green chemistry is the replacement of synthetic compounds with natural ones through the superior capitalization of natural resources, with numerous applications in different fields. The benefits of walnuts (Juglans regia L.) and elderberries (Sambucus nigra L.) have been known since ancient times, due to the presence of phytochemicals such as flavonoids, polyphenols, carotenoids, alkaloids, nitrogen-containing compounds, tannins, steroids, anthocyanins, etc. These active compounds have multiple biological activities for human health, including benefits that are antibacterial, antioxidant, anti-inflammatory, antidiabetic, hepatoprotective, antihypertensive, neuroprotective, etc. Like other medicinal plants, the walnut and the elderberry possess important phytosanitary properties (antibacterial, antifungal, and insecticidal) and their extracts can also be used as environmentally safe biopesticides, with the result that they constitute a viable and cheap alternative to environmentally harmful synthetic products. During recent years, walnut by-products and elderberries have attracted the attention of researchers, and investigations have focused on the species’ valuable constituents and active properties. Comparing the information from the literature regarding the phytochemical profile and biological activities, it is highlighted that, apart from the predominant specific compounds, the walnut and the elderberry have common bioactive compounds, which come from six classes (phenols and derivatives, flavonoids, hydroxycinnamic acids, tannins, triterpenoids, and phytosteroids), and act on the same microorganisms. From this perspective, the aim of this review is to provide an overview of the bioactive compounds present in the different constitutive parts of walnut by-products and elderberries, which present a specific or common activity related to human health and the protection of agricultural crops in the context of sustainable development.