Gold and silver nanoparticles have witnessed increased scientific interest due to their colourful colloidal solutions and exceptional applications. Comparing the localized surface plasmon resonance (LSPR) of gold and silver nanoparticles is crucial for understanding and optimizing their optical properties. This comparison informs the design of highly sensitive plasmonic sensors, aids in selecting the most suitable nanoparticles for applications like surface-enhanced infrared spectroscopy (SEIRA) and biomedical imaging, and guides the choice between gold and silver nanoparticles based on their catalytic and photothermal properties. Ultimately, the study of LSPR facilitates the tailored use of these nanoparticles in diverse scientific and technological applications. Two SEIRA methods combined with partial least squares regression (PLSR) chemometric tools were developed. This development is based on the synthesis of homogeneous, high-dense deposited metal nanoparticle islands over the surface of glass substrates to be used as lab-on-chip SEIRA sensors for the determination of bisacodyl (BIS) and its active metabolite in plasma. SEM micrographs revealed the formation of metallic islands of colloidal citrate-capped gold and silver nanoparticles of average sizes of 29.7 and 15 nm, respectively. BIS and its active metabolite were placed on the nanoparticles’ coated substrates to be directly measured, then PLSR chemometric modelling was used for the quantitative determinations. Plasmonic citrate-capped gold nanoparticle substrates showed better performance than those prepared using citrate-capped silver nanoparticles in terms of preparation time, enhancement factor, PLSR model prediction, and quantitative results. This study offers a way to determine BIS and its active metabolite in the concentration range 15–240 ng/mL in human plasma using inexpensive disposable glass-coated substrates that can be prepared in 1 h to get results in seconds with good recovery between 98.77 and 100.64%. The sensors provided fast, simple, selective, molecular-specific and inexpensive procedures to determine molecules in their pure form and biological fluid.