Display omitted •A new method for comparing nanoparticle capture efficiencies of biofilms is reported.•Nanoparticle size and surface functionalisation play a significant role in the capture.•P. putida shows superior entrapment efficiency for of all nanoparticles tested. The commercial use of nanoparticles has increased in recent years due to their unique characteristics, including high surface area, modifiable shape and surface charge and size-dependent properties. Consequently, a greater number of nanomaterials are now being released into the environment and inevitably interact with the natural ecosystem. Bacterial biofilms have the potential to capture and retain nanoparticles, however the factors determining the specific nanoparticle entrapment efficiencies of biofilms are not yet fully understood. Based on fluorescent intensity measurements we developed a simple and straightforward method that allowed the entrapment of different silica nanoparticles by two Pseudomonas strains to be quantified. It was determined that, regardless of nanoparticle size or surface functionalisation, Pseudomonas putida biofilms showed enhanced entrapment efficiencies compared to Pseudomonas fluorescens biofilms. It was also noted that both biofilms showed a higher entrapment capacity towards positively charged NPs. The method developed has the potential to be utilized for high throughput biofilm screening studies in order to develop a new understating of the relationship between nanoparticle characteristics and its uptake by bacterial biofilms.