There is increasing interest in the beneficial clinical effects of mindfulness-based interventions (MBIs). Research has demonstrated their efficacy in a wide range of psychological conditions characterized by emotion dysregulation. Neuroimaging studies have evidenced functional and structural changes in a myriad of brain regions mainly involved in attention systems, emotion regulation, and self-referential processing. In this article we review studies on psychological and neurobiological correlates across different empirically derived models of research, including dispositional mindfulness, mindfulness induction, MBIs, and expert meditators in relation to emotion regulation. From the perspective of recent findings in the neuroscience of emotion regulation, we discuss the interplay of top-down and bottom-up emotion regulation mechanisms associated with different mindfulness models. From a phenomenological and cognitive perspective, authors have argued that mindfulness elicits a "mindful emotion regulation" strategy; however, from a clinical perspective, this construct has not been properly differentiated from other strategies and interventions within MBIs. In this context we propose the distinction between top-down and bottom-up mindfulness based emotion regulation strategies. Furthermore, we propose an embodied emotion regulation framework as a multilevel approach for understanding psychobiological changes due to mindfulness meditation regarding its effect on emotion regulation. Finally, based on clinical neuroscientific evidence on mindfulness, we open perspectives and dialogues regarding commonalities and differences between MBIs and other psychotherapeutic strategies for emotion regulation.