The therapeutic potential of monoclonal antibodies (mAbs) makes them an ideal tool in both clinical and research applications due to their ability to recognize and bind specific epitopes with high affinity and selectivity. While mAbs offer significant therapeutic potential, their utility is overshadowed by the cost associated with their production, which often relies on the ability to identify minor antigen-specific cells out of a heterogeneous population. To address concerns with suboptimal methods for screening cells, we have developed a cell-sorting array composed of nanoliter spherical cell culture compartments termed microbubble (MB) wells. We demonstrate a proof-of-concept system for the detection of cell secreted factors from both immortalized cell lines and primary B cell samples. Exploiting the unique ability of the MB well architecture to accumulate cell secreted factors as well as affinity capture coatings, we demonstrate on-chip detection and recovery of antibody-secreting cells for sequencing of immunoglobin genes. Furthermore, rapid image capture and analysis capabilities were developed for the processing of large MB arrays, thus facilitating the ability to conduct high-throughput screening of heterogeneous cell samples faster and more efficiently than ever before. The proof-of-concept assays presented herein lay the groundwork for the progression of MB well arrays as an advanced on-chip cell sorting technology. © 2014 the Partner Organisations.