Transparent microelectrodes have emerged as promising tools to combine electrical and optical sensing and modulation modalities in many areas of biological and biomedical research. Compared to conventional opaque microelectrodes, they offer a number of specific advantages that can enable advances in functionality and performance. In addition to optical transparency, the mechanical softness feature is desired to minimize foreign body responses, increase biocompatibility, and avoid loss of functionality. In this review, we present recent research from the past several years on transparent microelectrode-based soft bioelectronic devices with an emphasis on their material properties and advanced device designs, as well as multimodal application scenarios for neuroscience and cardiology. First, we introduce material candidates with proper electrical, optical, and mechanical properties for soft transparent microelectrodes. We then discuss examples of soft transparent microelectrode arrays tailored to combine electrical recording and/or stimulation with optical imaging and/or optogenetic modulation of the brain and the heart. Next, we summarize the most recent progress on soft opto-electric devices integrating transparent microelectrodes with microscale light-emitting diodes and/or photodetectors into single and hybrid microsystems as powerful tools to explore the brain and heart functions. A brief overview of possible future directions of soft transparent microelectrode-based biointerfaces is provided to conclude the review.