Sprouts and microgreens have attracted tremendous interest across multiple disciplines in recent years. Here, we critically review the most recent advances to underscore research prospects and niches, and related challenges, not yet addressed or fully pursued. In particular, we report a number of themes that merit special attention as a result of their relevance to plant science, nutrition, health, and zootechnics: (1) species not yet or inadequately investigated, such as wild plants, and fruit tree strains; (2) abiotic and biotic factors, and biostimulants, for elicitation strategies and metabolic engineering; (3) sanitization and processing technologies to obtain high-quality products; (4) digestive fate and impact of bioactive elements, antinutrients, and allergens on human nutrition; (5) experimental challenges to researching health benefits; (6) the opportunity to generate natural product libraries for drug discovery; and (7) sprouts in animal feeding to improve both animal health and the nutritional value of animal products for the human diet. The convergence of different themes involving interdisciplinary competencies advocate fascinating research pursuits, for example, the elicitation of metabolic variants to generate natural product collections for identification and selection of bioactive chemicals with a role as nutraceuticals, key constituents of functional foods, or interactive partners of specific drugs.