Plasmonic nanoparticles enable manipulation and enhancement of light fields at deep subwavelength scales, leading to structures and devices for diverse applications in optics. Despite hybrid plasmonic materials display remarkable optical properties due to interactions between components in nanoproximity, scalable production of plasmonic nanostructures within a single-crystalline matrix to achieve an ideal plasmon-crystal interface remains challenging. Here, a novel approach is presented to realize efficient manipulation of in-lattice plasmonic nanoparticles. Employing ultrafast-laser-driven plasmonic nanolithography, metallic nanoparticles with controllable morphology are precisely defined in the crystalline lattice of yttrium aluminum garnet (YAG) crystal. Through direct ion implantation, hybrid plasmonic material composed of nanoparticles embedded in a sub-surface amorphous YAG layer is created. Subsequently, femtosecond laser pulses guide formation and reshaping of plasmonic nanoparticles from the amorphous layer into the single-crystalline matrix along direction of light propagation, facilitated by a plasmon-mediated evolution of laser energy deposition. By tailoring resonance modes and optimizing the coupling between structured particle assemblies, a range of applications including polarization-dependent absorption and nonlinearity, controllable photoluminescence, and structural color generation is demonstrated. This research introduces a new approach for fabricating advanced optical materials featuring in-lattice plasmonic nanostructures, paving the way for the development of diverse functional photonic devices.