Here we aimed to identify potential environmental and/or commercial management related chronic stressors for milkfish kept in marine cage systems using ontogenetic (OG) scale cortisol. We quantified OG scale cortisol as indicator for chronic stress levels in juvenile milkfish (average TL between 20 and 30 cm) from four cage systems (F1-F4; culture time: 2.5–3 months) with different geographic locations and management strategies within the mariculture area (approx. 2.2 × 0.6 km) of the Guiguiwanen Channel in Bolinao (Philippines). The sites were chosen along the mariculture area, with F1 located in the mouth of the channel, F2 at the beginning, F3 mid-way, and F4 at the end of the mariculture area. Each site was sampled twice (I, II) with a time interval of 15 days between both samplings. OG scale cortisol increased significantly between sampling I and II at all four sites, indicating that milkfish at all sites experienced to a certain extent stressful conditions within their cage system. At both samplings OG scale cortisol was highest at F4, where also the highest stocking density was observed. Taking into account the existing culture conditions, OG scale cortisol levels showed that different aspects of typically applied management strategies (e.g. stocking density, feeding strategy) as well as the location might have an effect on the stress level of cultured milkfish and therefore should be considered as potentially severe stressors in milkfish mariculture. To our knowledge this is the first study quantifying OG scale cortisol as indicator for chronic stress in commercial milkfish aquaculture settings, hereby contributing to overall more sustainable aquaculture practices.