Purpose <p>This paper examines the dynamic vibration analysis of a double FG porous sandwich microbeams system featuring a 2D periodic square holes (PSH) network, connected by an elastic medium and subjected to conditions involving a magnetic field and distributed adatoms. These conditions introduce a novel investigation into their combined impacts on adatoms-microbeam dynamics. The total interaction energy is presented using Morse and Lennard–Jones (6–12) potentials.</p> Methods <p>Based on the Euler–Bernoulli model (EBM), the coupled dynamic vibration theory and nonlocal material elasticity are integrated to develop a novel model for the composite behavior of functional microsystem. The fundamental coupled equations are derived and solved analytically through a Navier-type solution (NTS) approach and numerically using the differential quadrature method (DQM).</p> Results <p>Analyses of functional double microsystem vibration indicate a decrease in nonlocal frequency with an increase in the nonlocal parameter and gradient index. The results indicate that both methods converge and are effective for solving the governing equation. The dynamic response is influenced by the applied conditions of the multiphysics parameters. Notably, there is an apparent discrepancy in frequency shift values compared to those observed in a single functional microsystem.</p> Conclusions <p>The nonlocal EB functional model outperforms standard EBM in predicting dynamic behavior by accounting for both the small-scale effect and coupling dynamics. The integration of complex configuration and interatomic interaction is a distinctive feature of the functional double microsystem and represents an essential point in this contribution. The derived system in this paper is well-suited for investigating the dynamic response of adatom microsystems.</p>