Multifunctional, plasmonically-active nanorods based on gold cores and silver shells (AuNR/Ag), after exposure to tomato plants, were found to be taken up in rather short times, being detected by SERS in both roots and stems, while exhibiting lack of phytotoxicity in the concentrations used during this study. Additionally, we report that AuNR/Ag have the ability to deliver auxin growth regulator 2,4-D, which resulted in a significant impact on the regulation of tobacco cell culture growth. The unique morphology of these nanorods allowed their sensitive SERS detection, resulting in a technological approach that combines both high-sensitivity detection and delivery of biologically active molecules to plant tissues or cells. Here, we demonstrate that the multiplex combination of plasmonically active agents, laser spectroscopy, and plant biology could represent a new direction in bio-nano-engineering that integrates the use of spectroscopically-active systems for delivery of active compounds and ultra-sensitive detection in plants.