The generation of nanoparticles using pulsed laser ablation has inherent advantages compared to conventional methods, like the purity and stability of the fabricated nanoparticle aerosols and colloids. This study addresses the influence of the pulse energy on the nanoparticle productivity and particle size during femtosecond laser fabrication of nanoparticles in air and liquids (water, hexane). Moreover, in-situ conjugation of nanoparticles in hexane is studied. The nanoparticle generation rate is 100 times higher in air compared to water. Higher pulse energies lead to higher productivity, but due to shielding effects, the optimum was determined at moderate pulse energies around 200 µJ, measured by the highest absorption intensity of the plasmon resonance of the colloids. In non-polar liquid, the in-situ conjugation of gold nanoparticles to thiol molecules during pulsed laser ablation is studied. At higher concentrations (8 mmol/l) of dodecanethiol in n-hexane solution, significant smaller nanoparticles (30 nm) and less agglomerates are generated.