Lignin-based nano- and microcarriers are a promising biodegradable drug delivery platform inside of plants. Many wood-decaying fungi are capable of degrading the wood component lignin by segregated lignases. These fungi are responsible for severe financial damage in agriculture, and many of these plant diseases cannot be treated today. However, enzymatic degradation is also an attractive handle to achieve a controlled release of drugs from artificial lignin vehicles. Herein, chemically cross-linked lignin nanocarriers (NCs) were prepared by aza-Michael addition in miniemulsion, followed by solvent evaporation. The cross-linking of lignin was achieved with the bio-based amines (spermine and spermidine). Several fungicides—namely, azoxystrobin, pyraclostrobin, tebuconazole, and boscalid—were encapsulated in situ during the miniemulsion polymerization, demonstrating the versatility of the method. Lignin NCs with diameters of 200–300 nm (determined by dynamic light scattering) were obtained, with high encapsulation efficiencies (70–99%, depending on the drug solubility). Lignin NCs successfully inhibited the growth of Phaeomoniella chlamydospora and Phaeoacremonium minimum, which are lignase-producing fungi associated with the worldwide occurring fungal grapevine trunk disease Esca. In planta studies proved their efficiency for at least 4 years after a single injection into Vitis vinifera (“Portugieser”) plants on a test vineyard in Germany. The lignin NCs are of high interest as biodegradable delivery vehicles to be applied by trunk injection against the devastating fungal disease Esca but might also be promising against other fungal plant diseases.