Noble metal nanostructures have demonstrated many intriguing features for both therapy and diagnosis in a number of diseases. However, their clinical translation is prevented by their accumulation in organisms that can result in toxicity and interference with common medical diagnoses. In order to combine the most interesting behaviour of metal nanoparticles with the possibility of their body clearance, we have recently introduced and tested the passion fruit-like nano-architectures. They are versatile 100 nm biodegradable nanostructures composed by a silica shell embedding functional polymeric arrays of ultra-small noble metal nanoparticles. Here, we report a novel simple and robust protocol to increase the loading of ultra small gold nanoparticles in the nano-architectures, promoting their possible application in clinical diagnosis.