The stability of free-standing nanobubbles is a long-standing controversial problem due to the Laplace pressure catastrophe at the nanoscale. In most industrial circumstances, a large quantity of surfactants is required as stabilisers or emulsifiers to generate stable bubbles or foams. However, when surfactants exceed a certain level, they can adversely affect living organisms and pose environmental risks. Towards biomedical use, we investigated nanobubble generation through a mini-extruder in amino acid solutions. Herein, we considered glycine (having two pKa values) and lysine (having three pKa values) as two model amino acids, conducting experiments with various concentrations (0.1M, 0.5M and 1M), along with different pH values (above, equal to, and below the isoelectric points of each amino acids; 5.97 for glycine and 9.74 for lysine). Our results showcased the proof of concept that amino acids can stabilise nanobubbles in bulk for a few days. We achieved remarkable products of nanobubbles via nanopores by extrusion, with reproducible size distribution and stability. We also compared the extrusion protocol with the commonly used ultrasound method. It turned out that extrusion generated samples with smaller sizes and higher concentrations than sonication. This study provides a reliable protocol for generating small-scale nanobubbles for biomedical use, showing great potential in drug delivery for medical treatment.