Gold (Au) nanoparticles (NPs) have large surface areas and novel optical properties and can be readily functionalized using thiol-based chemistry; hence, they are useful in bioanalytical chemistry. Here, we describe a one-step, plasma-etching process that results in the spontaneous formation of Au NP coated recessed microstructures in silicon (Si). Mechanistically, the plasma etch rate of Si was enhanced in the vicinity of 10-100 nm thick Au patterns resulting in the formation of microwells or microchannels uniformly coated with 20-30 nm sized Au NPs. The methodology provides versatility in the types of microstructures that can be formed by varying the shape and dimensions of the Au patterns and the etch time. We also describe selective binding of antibodies to Au NP coated Si microwells using thiol-based surface modification.