Classical assessments of new fish feeds are anthropocentric, focusing mainly on growth. Although this methodology is accurate, it does not consider the fish' perspective. This study aimed to investigate the behavioural responses and feed preferences of Nile tilapia (Oreochromis niloticus) and gilthead seabream (Sparus aurata) through a self-selection trial using self-feeders. Both species were offered three feeds: a control (PD) commercial-like feed and two diets (ORG1 and ORG2) formulated with different inclusions of alternative ingredients to address some of the current environmental concerns and/or ethical issues often associated with commercial formulations. Three groups of tilapia with an average weight of 163.0 g ± 4.3 g (mean ± SD) and four groups of seabreams with 174.7 g ± 27.0 g were tested. Tilapia exhibited a preference for ORG2 (46.5%), influenced by the sensory properties of the feed and post-ingestion signals. Seabream did not show a preference for any feed. These findings highlight the effectiveness of self-selection experiments in allowing fish to express their feeding behaviour and preferences. Therefore, this approach should be considered in the initial screening and design of new aquaculture feeds and ingredients.