The early, rapid, and reliable diagnosis of a pathological condition is of critical importance for the subsequent treatment of a patient. Molecular diagnostic methods using biomarkers are increasingly advancing due to their non-invasive nature and are greatly benefited by the implementation of microsystems, as minute amounts of sample can be analyzed in a quick, cost-effective and highly sensitive way. Still a challenging feature is multiplexity in analysis: diseases like tumor, cardiovascular, Alzheimer’s, are related to not only one but several biomarkers which should all be addressed in a test in order to assess reliably the patient’s condition. This work describes an acoustic wave microsystem integrating microfluidics to compartmentalize its surface into discrete domains and achieve multiplicity. The development steps are described from concept to design, fabrication, evaluation, and proof-of-principle through detection of four protein cardiac markers. The sensitivity and reproducibility of the sensing domains, as well as the highly selective capture of the desired biomarkers are very promising for the development of the system into an integrated lab-on-chip diagnostic platform.