Anaerobic digestion (AD) is a well-established method for waste/wastewater treatment and biogas production, but challenges remain in improving its performance, particularly for toxic/inhibitory organic compounds such as lipids, hydrocarbons, polyphenols, pharmaceuticals, and other pollutants. Micro-aeration, which involves the controlled introduction of small amounts of oxygen, has emerged as a promising strategy to enhance microbial activity, stimulate the degradation of challenging compounds, and improve methane yields. This review addresses the different strategies used for effective oxygen dosing, measurement, and control, while also delving into the bioenergetics of the coexisting anaerobic and micro-aerobic pathways. Studies demonstrating the potential of micro-aeration to enhance the anaerobic treatment of recalcitrant organic pollutants, such as BTEX (benzene, toluene, ethylbenzene, and xylene) and pharmaceutical compounds, are reviewed. Several works use micro-aeration as a pretreatment, while those implementing it directly within bioreactors typically apply it intermittently. Nevertheless, in most cases, the application of micro-aeration is guided by a "trial-and-error" approach, and a systematic understanding of optimal strategies and dosing for different classes of pollutants remains lacking. The review also explores the diverse roles of micro-aeration in the AD of lipids, highlighting key microorganisms and underlying mechanisms that drive these processes, for instance, the role of facultative anaerobes in converting oleate into palmitate and protecting methanogenic communities. Finally, this work highlights future directions and remaining challenges in applying micro-aeration for the anaerobic treatment of organic pollutants. KEY POINTS: AD of lipids, hydrocarbons, dyes, pharmaceuticals, and other pollutants is challenging. Micro-aeration reshapes microbial communities and enhances pollutant degradation. Effective micro-aeration depends on several factors and is not fully mastered.