Gold nanoprisms possess remarkable optical properties that make them useful for medical biotechnology applications such as diagnosis and photothermal therapy. However, shape-selective synthesis of gold nanoprisms is not trivial and typically requires either toxic surfactants or time-consuming purification protocols, which can limit their applicability. Here, we show how triangular gold nanoprisms of different sizes can be purified by precipitation using the non-toxic glutathione ligand, thereby removing the need for toxic surfactants and bottleneck purification techniques. The protocol is amenable for direct scaling up as no instrumentation is required in the critical purification step. The new purification method provides a two-fold increased yield in gold nanoprisms compared to electrophoretic filtration, while providing nanoprisms of similar localized surface plasmon resonance wavelength. Crucially, the gold nanoprisms isolated using this methodology show fewer non-specific interactions with cells and lower cellular internalization, which paves the way for a higher selectivity in therapeutic applications.