Legume-rhizobial symbiosis, involving the intracellular accommodation of rhizobia within host cells for nitrogen fixation, represents a unique model among plant-microbe interactions. While this symbiosis requires sophisticated regulatory networks, direct host control over symbiont proteins remains largely elusive. Here, we demonstrate that soybean Nodulation Receptor Kinase (GmNORK) interacts with and directly phosphorylates the Sinorhizobium fredii HH103 effector NopZ. This host-mediated phosphorylation promotes NopZ nuclear/perinuclear enrichment and is associated with enhanced NopZ interaction with the nucleoporin GmNENA at the nuclear envelope/nuclear pore complex, establishing a key signaling step that links membrane-proximal symbiotic signaling to the nuclear pore. Expression of phosphomimetic NopZ variants enhances soybean nodulation, whereas GmNENA-silencing in soybean roots reduces nodule numbers. Our findings reveal a previously unknown model for plant-microbe interactions, where the direct phosphorylation of a bacterial effector by a host receptor kinase provides an essential regulatory mechanism to direct effector localization and promote the symbiotic program.