Transmembrane proteins play important roles in intercellular signaling to regulate interactions among the adjacent cells and influence cell fate. The study of interactions between membrane proteins and nanomaterials is paramount for the design of nanomaterial-based therapies. In the present work, the fluorescence properties of the transmembrane receptor Notch2 have been investigated. In particular, the steady-state and time-resolved fluorescence methods have been used to characterize the emission of tryptophan residues of Notch2 and then this emission is used to monitor the effect of silver colloids on protein behavior. To this aim, silver colloids are prepared with two different methods to make sure that they bear hydrophilic (citrate ions, C-AgNPs) or hydrophobic (dodecanethiol molecules, D-AgNPs) capping agents. The preparation procedures are tightly controlled to obtain metal cores with similar size distributions (7.4 ± 2.5 and 5.0 ± 0.8 nm, respectively), thus, making the comparison of the results easier. The occurrence of strong interactions between Notch2 and D-AgNPs is suggested by the efficient and statistically relevant quenching of the stationary protein emission already at low nanoparticle (NP) concentrations (ca. 12% quenching with [D-AgNPs] = 0.6 nM). The quenching becomes even more pronounced (ca. 60%) when [D-AgNPs] is raised to 8.72 nM. On the other hand, the addition of increasing concentrations of C-AgNPs to Notch2 does not affect the protein fluorescence (intensity variations below 5%) indicating that negligible interactions are taking place. The fluorescence data, recorded in the presence of increasing concentrations of silver nanoparticles, are then analyzed through the Stern–Volmer equation and the sphere of action model to discuss the nature of interactions. The effect of D-AgNPs on the fluorescence decay times of Notch2 is also investigated and a decrease in the average decay time is observed (from 4.64 to 3.42 ns). The observed variations of the stationary and time-resolved fluorescence behavior of the protein are discussed in terms of static and collisional interactions. These results document that the capping shell is able to drive the protein–particle interactions, which likely have a hydrophobic nature.