Involved in peroxisomal beta-oxidation of branched-chain fatty acids (BCFAs) and bile acids intermediates. Catalyzes the initial and rate-limiting dehydrogenation step that removes two hydrogen molecules and introduces a trans double bond between the alpha and beta carbons of the acyl CoA molecules while generating hydrogen peroxide as a by-product. Oxidizes its substrates in a stereospecific way and can only desaturate isomers carrying (2S)-methyl groups (By similarity) (PubMed:29287774). In brown adipose tissue peroxisomes, mediates beta- oxidation of monomethyl branched-chain fatty acids with iso configuration (mmBCFAs) as part of a substrate synthesis and oxidation cycle fueled by FASN-dependent de novo mmBCFA synthesis. The mmBCFA catabolism is coupled to AMPK activation and mitochondrial ATP production as a thermogenic adaptation mechanism to maintain the body temperature in cold environment (By similarity). Metabolizes multi- methyl-branched fatty acyl-CoA esters such as (2S)-pristanoyl-CoA, displaying redundancy with ACOX3 (PubMed:29287774). In the liver, mediates side-chain beta-oxidation of C27 bile acyl-CoA intermediates carrying a (25S)-methyl group to yield 24,25-trans unsaturated derivatives as part of peroxisomal bile acid synthesis pathway (PubMed:27884763, PubMed:29287774). Can oxidize straight-chain fatty acyl CoAs such as C10-CoA and C16-CoA with low efficiency (PubMed:29287774). {ECO:0000250|UniProtKB:Q9QXD1, ECO:0000269|PubMed:27884763, ECO:0000269|PubMed:29287774}. This is the function of ACOX2 (acyl-CoA oxidase 2, ENSG00000168306).