<p>Prevalence of promoter paused R loops formed from frequent RNA PolII pausing in eukaryotic cells not only pose a significant threat to genomic stability, but also a potent regulator of transcription. In this review, we discuss how R loops act as both a product and regulator of transcription. Direct effects of R loops on transcription output are not well established, as studies on R loops are mainly focused on genomic instability triggered by accumulation of R loops. We dissect the evidence showing how R loops regulate transcription through a new manner: transcription condensates. Transcription condensates are dynamic, membraneless assemblies enriched with components of the transcription machinery, transcription factors, coactivators, and RNA-binding proteins (RBPs) that form at regulatory loci of critical, highly expressed genes to promote transcription rapidly and robustly. Coinciding at these condensate-forming regulatory loci are R loop hotspots, but this relationship and how they impact transcription as a unit remain to be defined. Recent developments suggest that R loops may act as multivalent seeds for transcription condensates through its modular structure, and as a binding platform for numerous RBPs containing phase separation-prone disordered regions. Interestingly, R loop processing may act as a double-edged sword to transcription: with partitioning of some factors into the transcription condensate promoting transcription, while others terminating transcription as a trade-off for protecting genomic integrity against pervasive R loops. Finally, we also summarize pathological conditions involving alterations of factors implicated in both R loop homeostasis and condensate dysregulation.</p>