The Northeast Atlantic mackerel (Scomber scombrus) is a zooplanktivorous fish with its main summer feeding grounds in the waters around Iceland. The zooplankton in the stomachs of the caught fish causes several problems during processing due to the high enzyme activity of the zooplankton. The aim of the study was to evaluate the chemical characteristics of zooplankton that accompanies mackerel as a side-catch and stomach fullness as affected by catching year, season, catching zone, and catching method over three mackerel seasons from 2016 to 2018. Species identification by the fatty acid tropic marker method (FATM) was also applied within the zooplankton rich side-stream. FATM analysis indicated that the majority of the zooplankton mass belonged to Calanus finmarchicus. The lipid composition of the zooplankton rich side-stream varied between years but was rich in monounsaturated, as well as polyunsaturated fatty acids (PUFA), such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). The results suggest that the zooplankton rich side-stream from mackerel caught in Icelandic waters has the potential for further sustainable processing into valuable nutrients.