Graphene-encapsulated metal nanoparticles (G@NPs) offer a possibility to observe confined reactions in the nanocontainer formed by the NP’s facets and graphene. However, direct experimental detection of adsorbed atomic and molecular species under the graphene cover is still challenging, and the mechanisms of intercalation and adsorption are not well understood. Here, we show that Kelvin probe force microscopy can largely contribute to the understanding of adsorption and desorption at the single NP level, which we exemplify by comparing oxygen adsorption experiments obtained at as-prepared PdNPs and G@PdNPs, both supported on highly oriented pyrolytic graphite and studied under ultrahigh vacuum (UHV) conditions. We show that oxygen adsorption at room temperature occurs at a much higher partial oxygen pressure on G@PdNPs compared to as-prepared PdNPs. Similarly, the removal of oxygen via a reaction with the residual gas of the UHV is slower on the G@PdNPs compared to as-prepared PdNPs. The differences can be explained by a limited facility for reactant and product molecules to enter and desorb from the nanocontainer via the defects of the graphene. Experimental observations are supported by assisting density functional theory calculations.