Major scientific discoveries in the last two decades have been enabled by the development of high-throughput sequencing and mass spectrometry (MS) technologies. Omics analysis, at the genome, transcriptome, proteome, or metabolome levels, has paved the way for the elucidation of many molecular mechanisms that underlie disease, biomarker and drug-target discovery, and diagnostics and precision medicine applications. With the realization that the biological interpretation of results generated from biological tissues or cell-derived samples is highly impacted by cell heterogeneity, many efforts have been redirected toward the omics characterization of single cells. As miniaturized devices represent ideal platforms for the analysis of small sample amounts, omics analysis has found a flourishing ground in the microfluidics instrumentation development arena. This Review aims at capturing the latest protein and proteome analysis technologies that have been developed and implemented on microfluidic platforms, with a focus on developments that have been documented in the past two years. Emphasis was placed on challenging aspects that relate to sensitivity and handling sample complexity, as well as on applications that address demanding biological and biomedical problems.