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Plastids (chloroplasts), mitochondria, and peroxisomes are subcellular organelles with essential roles in energy capture, conversion, and metabolism, among many pivotal cellular processes. The biogenesis, protein targeting, proliferation, and degradation of these organelles are highly regulated in the plant cell. Several metabolic pathways, including photosynthesis and photorespiration, and the metabolism of fatty acids and derivatives, are attributed to the functional coordination of these organelles. In addition, plastids are key hubs for emitting multiple retrograde signals to regulate nuclear gene expression in response to developmental and environmental cues. Emerging evidence also points to the role of these organelles as environmental sensors involved in the balance between plant growth and defense. This Research Topic consists of 4 original research articles and 4 review articles that highlight recent advances in the understanding of the dynamics and the metabolic and signaling functions of the three energy organelles, as well as inter-organellar crosstalk and networking. How to improve crop yield through regulating photosynthetic assimilate distribution and source-sink balance is also discussed.