Biosensor's ability depends on both platform performance and surface modification. In mass sensitive biosensors, a stable coating with molecular structural dynamism increases sensitivity. Also, its orientation and smoothness directly affect the performance of cross-linker molecules and receptors. In this study, the performance of intact double-layered (ID) coating used on QCM−D for the first time in DNA detection of MPS was investigated. The sensitivity of the QCM−D with ID-MPS was compared to the uncoated. At the concentrations of 1010 and 1013 copies/mL, the method with ID-MPS was approximately 6.4 times more sensitive. A shift of 1.22(±0.42) Hz was observed at the detection limit at 108 copies/mL, while it was 0.19(±0.05) Hz in the negative control. Thus, a signal-to-noise-ratio greater than 3, which is a measure of signal quality in biosensors, was exceeded with a ratio of 3.33, and it was shown that the detection signal at the sensitivity limit was sufficient. In addition, the two methods were compared visually with atomic force microscopy in terms of the amount and distribution of captured molecules, and it was determined that the ID-MPS was more efficient.