Sputtered reactive multilayers applied as a heat source in electronic joining processes are an emerging technology. Their use promises low-stress assembly of components while improving thermal contact and reducing thermal resistance. Nanostructured surface modifications can significantly enhance adhesion and reliability of joints between different materials. This work examines reactive multilayer of nickel and aluminum, directly sputtered on nanostructured black silicon surfaces and compares their phase transformation with reference samples deposited on pristine silicon surface. The investigation of the quenched self-propagating reaction reveals a clear influence of the nanostructured surface on the prolongation of the phase transition. Rapid thermal annealing tests result in the formation of Al1.1Ni0.9 phase. The nanostructured interface seems to hinder the full transformation of the parent material. The surface modification improves the adhesion of the formed alloy on silicon surfaces and can possibly increase the reliability of joints based on reactive aluminum/nickel multilayer. The use of black silicon, a nanostructured surface modification, is thus a promising approach to realize reliable multi-material joints in complex systems.