In-situ functionalization of gold nanoparticles with fluorophore-tagged oligonucleotides is studied by comparing femtosecond laser ablation in stationary liquid and in biomolecule flow. Femtosecond laser pulses induce significant degradation to sensitive biomolecules when ablating gold in a stationary solution of oligonucleotides. Contrary, in-situ conjugation of nanoparticles in biomolecule flow considerably reduces the degree of degradation studied by gel electrophoresis and UV–Vis spectrometry. Ablating gold with 100 μJ femtosecond laser pulses DNA sequence does not degrade, while the degree of fluorophore tag degradation was 84\% in stationary solution compared to 5\% for 1 mL/min liquid flow. It is concluded that femtosecond laser-induced degradation of biomolecules is triggered by absorption of nanoparticle conjugates suspended in the colloid and not by ablation of the target. Quenching of nanoparticle size appears from 0.5 μM biomolecule concentration for 0.3 μg/s nanoparticle productivity indicating the successful surface functionalization. Finally, increasing the liquid flow rate from stationary to 450 mL/min enhances nanoparticle productivity from 0.2 μg/s to 1.5 μg/s, as increasing liquid flow allows removal of light absorbing nanoparticles from the ablation zone, avoiding attenuation of subsequent laser photons.