Aluminum nitride-based MEMS resonators are one of the interesting recent research topics for its tremendous potential in a wide variety of applications. This paper focuses on the detrimental effect of residual stress on the AlN based MEMS resonator design for acoustic applications. The residual stress in the sputtered c axis (<001>) preferred oriented AlN layers on Si (111) substrates are studied as a function of layer thickness. The films exhibited compressive residual stresses at different thickness values: -1050 MPa (700 nm), -500 MPa (900 nm), and -230 MPa (1200 nm). A mushroom-shaped AlN based piezoelectric MEMS resonator structure has been designed for the different AlN layer thicknesses. The effect of the residual stresses on the mode shapes, resonant frequencies, and quality factor (Q) of the resonator structures are studied. The resonant frequency of the structures are altered from 235 kHz, 280 kHz, and 344 kHz to 65 kHz, 75 kHz and 371 kHz due to the residual stress of -1050 MPa (thickness: 700 nm), -500 MPa (thickness: 900 nm) and -230 MPa (thickness: 1200 nm) respectively. At no residual stress, the quality factors of the resonator structures are 248, 227, 241 corresponding to the 700 nm, 900 nm, and 1200 nm thick AlN layers respectively. The presence of the residual stress reduced the Q values from 248 (thickness: 700 nm), 227 (thickness: 900 nm), 241 (thickness: 1200 nm) to 28, 53, and 261 respectively.