Biofilms are complex environments where matrix effects from components such as extracellular polymeric substances and proteins can strongly affect SERS performance. Here the interactions between SERS-enhancing Ag and Au particles were studied using ex situ biofilms (es-biofilms), which were more homogenous than in situ biofilm samples. This allowed systematic quantitative studies, where samples could be accurately diluted and analysed, to be carried out. Strong signals from intrinsic marker compounds were found for the Pseudomonas aeruginosa and Staphylococcus aureus extracted es-biofilms, which the standard addition method showed were due to 2 × 10-3 mol dm-3 pyocyanin or the equivalent of 1 × 10-4 mol dm-3 adenine, respectively. The es-biofilms hindered aggregation of Ag colloids more than Au but for both Au and Ag nanospheres the presence of es-biofilm reduced SERS signals through a combination of poorer aggregation and blocking of surface sites. For Ag, the effect of lower aggregation was to reduce the signals by a factor of ca. 2×, while site blocking gave a further 10× reduction for adenine. Similar results were found for Au nanospheres with adenine, although these particles gave low enhancement with pyocyanin. Nanostars were found to be unaffected by reduced aggregation and also showed lower site blocking effects, giving more reproducible signals than those from aggregated particles, which compensated for their lower enhancement factor. These results provide a rational basis for selecting enhancing substrates for use in in situ studies, where the further complexity means that it is important to begin with well-understood and controllable enhancing media.