This paper presents a novel fabrication process that allows integration of polydimethylsiloxane (PDMS)-based microfluidic channels and metal electrodes on a wafer with a micrometer-range alignment accuracy. This high level of alignment accuracy enables integration of microwave and microfluidic technologies, and furthermore accurate microwave dielectric characterization of biological liquids and chemical compounds on a nanoliter scale. The microfluidic interface between the pump feed lines and the fluidic channels was obtained using magnets fluidic connection. The tube-channel interference and the fluidic channel-wafer adhesion was evaluated, and up to a pressure of 700 mBar no leakage was observed. The developed manufacturing process was tested on a design of a microwave-microfluidic capacitive sensor. An interdigital capacitor (IDC) and a microfluidic channel were manufactured with an alignment accuracy of 2.5 µm. The manufactured IDC sensor was used to demonstrate microwave dielectric sensing on deionized water and saline solutions with concentrations of 0.1, 0.5, 1, and 2.5 M. Author Contributions: Conceptualization, J.B. and T.M.; methodology, J.B., L.B., and D.K. ; validation, J.B. and T.M.; data curation, J.B.; writing-original draft preparation, J.B. and T.M.; writing-review and editing, J.B., T.M., L.B., D.K., I.O., R.P., and B.N.; visualization, T.M.; supervision, I.O. and B.N.; and funding acquisition, T.M., I.O., R.P., and B.N. All authors have read and agreed to the published version of the manuscript.