The dynamic process of intracellular reduction-oxidation status (redox homeostasis) is influenced by various factors, with mitochondria being one of the most significant contributors. Mitochondria play a crucial role in the bioenergetic pathway, fulfilling the metabolic energy demands of cells. To maintain increased energy requirements, mitochondrial biogenesis and fusion are employed, while decreased energy demands or damaged mitochondria are addressed through fission and autophagic removal, known as mitophagy. Any disruption in these adaptive responses can compromise redox homeostasis and cellular function, and make cells more vulnerable to oxidative stress, resulting in oxidative DNA damage, inflammatory responses, and apoptotic/anti-apoptotic reactions. Such dysregulation contributes to the development of “free radical diseases” like metabolic disorders and cancer. Traditional medicines and herbs (possessing antioxidant and autophagic properties) have been utilized for centuries in the treatment of various diseases; however, it is only recently that researchers have begun to investigate their molecular, cellular, and tissue-level modes of action. Nevertheless, concerns about their cytotoxicity have also arisen. This manuscript focuses on the current technological advancements in assessing the properties of plant-based natural compounds. Both cell-free and cell-based methods are employed to evaluate the therapeutic potential of these compounds, allowing for their scientific evaluation and validation.