Agricultural disease control faces serious hurdles due to the increasing resistance of pathogens and the banning of synthetic plant protection products (PPPs), resulting in environmental and public health risks. In this context, biodegradable nanocarriers derived from macroalgae (Bio-MACs), such as functional polysaccharides and proteins (e.g., alginic acids, chitosans, and carrageenans), offer promising technical solutions. The efficient encapsulation and controlled release of bioactive metabolites with antifungal, antibacterial, and biostimulant properties can be achieved using these nanocarriers. The developed systems protect the active ingredients from degradation, prolong their efficacy in soil, and minimize soil and water contamination by reducing application doses by up to 40%. Furthermore, these systems exhibit low toxicity to non-target organisms, such as Daphnia magna and Eisenia fetida, in accordance with the OECD TG 202 and 207 guidelines. Bio-MACs have regulatory advantages over synthetic nanoparticles because they are generally recognized as safe (GRAS), non-toxic, non-reactogenic, widely available and highly biodegradable. These characteristics make them uniquely suited for use in the food and agricultural industries, where sustainability is critical. Moreover, the economic potential and marketability of Bio-MACs are booming, particularly given the rising demand for eco-friendly agricultural inputs and the rapid expansion of the biopesticides sector, which is set to hit USD 10 billion by 2027. However, successful market integration requires acknowledging and addressing challenges such as public and regulatory concerns surrounding nanotechnology. This requires standardizing production protocols and conducting large-scale field trials to demonstrate the effectiveness and safety of nanotechnology. Thus, the objective of this systematic review is to explore the potential of Bio-MACs for encapsulating and releasing biological metabolite activities.