This paper presents a differential-mode microwave microfluidic sensor useful for the characterization/detection of the denaturation of Bovine Serum Albumin (BSA), a protein with numerous biochemical applications, caused by a chaotropic agent, specifically, urea. The sensor consists of a pair of uncoupled microstrip lines, each one loaded with a transversally oriented slot resonator, etched in the ground plane. The sensor is a device able to detect permittivity changes in the so-called material under test (MUT), or liquid under test (LUT), as compared to a reference (REF) material/liquid. However, since the changes in the permittivity of the BSA caused by the denaturation process are partially obscured by the presence of the urea in the LUT, a protocol to separate the effects of the urea in the sample is proposed. According to such protocol, two different BSA samples, with different concentrations, are needed. It is shown that, with such a method, the denaturation process can be detected and characterized through the so-called hydration contrast, related to the measured difference of the output variables (the cross-mode transmission coefficient) in both BSA samples. The reported protocol and denaturation detection method based on differential-mode microwave sensing, which has never been reported so far, provides hydration contrasts of 0.06 for 6M urea concentrations.