Prestress, which is critical to prestressed concrete (PC) structures, can be monitored using resonance-enhanced magnetoelastic (REME) sensors. REME sensors inside the PC structure are influenced by adjacent sensors and adjacent rebars. However, the sensor’s anti-electromagnetic interference (EMI) encapsulation is lacking. After clarifying the principle of the REME method, a finite element model was established. The influence of the encapsulation’s electrical conductivity and magnetic permeability on the sensor’s electromagnetic compatibility was analyzed. Prestress monitoring experiments were conducted. The results showed that the sensor encapsulated with brass can resist low-frequency EMI and high-frequency EMI. After encapsulating, the sensitivity of the induced voltage-prestress relationship to adjacent sensors was reduced by 52.07%, and that to adjacent rebars was increased by 14.54%. The corresponding prestress monitoring accuracy was increased by 20.86% and 24.49%, respectively. The higher monitoring accuracy verified the feasibility of the proposed encapsulation method, which can resist both low-frequency EMI and high-frequency EMI.