Size control of laser-fabricated surfactant-free gold nanoparticles is a challenging endeavor. In this work, we show that size control can be achieved by adding ions with low salinity during synthesis. In addition, this approach offers the opportunity to fundamentally study ion interactions with bare nanoparticle surfaces and can help to elucidate the nanoparticle formation mechanism. The studies were carried out in a flow-through reactor and in the presence of NaCl, NaBr and sodium phosphate buffer at minimal ionic strengths. A significant size quenching effect at ionic strengths from 1–50 μM was found, which allowed surfactant-free nanoparticle size control with average diameters of 6–30 nm. This effect went along with low polydispersity and minimal aggregation tendencies and was confirmed by UV-vis spectroscopy, TEM, SEM and analytical disk centrifugation. Our findings indicate that size quenching originates from an anionic electrostatic stabilization depending on the nanoparticle surface area, which may be caused by specific ion adsorption. By subsequent delayed bioconjugation in liquid-flow using bovine serum albumin as a stabilizing agent, nano-bioconjugates with good stability in cell culture media were obtained, which are applicable in toxicology and cell biology.