<p>This investigation explores how the resonance frequency of a simply supported biomolecular resonator changes due to adsorption-driven thermomagnetic phenomena. The system studied is a five-layer smart sandwich nanobeam consisting of a ceramic core, two perforated face layers with a two-dimensional square hole network, and outer adhesive, functionally graded porous layers. A new model has been developed to capture the adsorption energy of bio-receptors and spike proteins, incorporating van der Waals forces and surface stresses to accurately describe multiphysics interactions. The dynamic behavior is modeled using Timoshenko nonlocal beam theory, enhanced by strain gradient effects, residual axial stress, and Lorentz magnetic forces generated by a longitudinal magnetic field. Adsorption energy is estimated using both Morse and Lennard–Jones (6–12) potentials. By applying Hamilton’s principle, the governing equations are derived to include shear deformation, surface effects, and interatomic interactions. These equations are then solved analytically using the Navier method and numerically via the differential quadrature method. The resonance frequency shift is shown to be strongly influenced by surface properties, geometric and perforation parameters, porosity, adatom distribution, and thermomagnetic field strength. Interatomic forces cause a softening effect, reducing the system’s stiffness and lowering the resonance frequency. The high agreement between analytical and numerical results confirms the model’s accuracy. This nonlocal strain gradient approach offers a valuable tool for predicting the vibrational behavior of nanoscale resonators. It is especially relevant for biomolecule sensing applications, such as measuring viral spike protein density and mass. The study underscores the critical influence of adsorption and thermomagnetic coupling in the dynamics of nanosystems.</p>