This work presents a novel dual-mode charge and refractive index sensitive device integrated with nanoplasmonic islands, for the first time, on insulator-semiconductor junctions. The developed nano-metal-insulator semiconductor (nMIS) sensor facilitates simultaneous detection of charge and mass changes on the nanoislands due to the binding of biomolecules. The charging of the nanoislands is traced by using the capacitive field-effect electrolyte-metal-insulator-semiconductor structure and the refractive index changes are quantified by measuring the change in the localized surface plasmon resonances of the nanoislands. To demonstrate the performance of our dual-mode sensor we study the effect of oxygen plasma on immobilized biomolecules. As a case study biotinylated aptamers specific to interleukin 6 (IL-6) were chosen to conduct the immunoassay studies. We confirm that the adsorbed aptamers on the nanoislands do not lose their functionality after exposure to low energy oxygen plasma (<600 J). This finding is critical for the development of 'ready-to-use' microfluidic immunoassay platforms (glass-PDMS based) where immobilizing biomolecules on one of the substrates is often required prior to the bonding of glass and PDMS. Our results also open new opportunities for utilizing plasma to encapsulate biomolecules in polymers and hydrogels. More significantly, nMIS sensors can readily be adopted for multiplexed and high throughput label free immunoassay systems, further driving innovations in biomedical and healthcare research.