Domestication and selective breeding can mitigate current bottlenecks in European perch aquaculture. Monitoring the condition and stress tolerance of European perch stocks from different recirculating aquaculture systems is of general interest to set the baseline values of promising candidates for further breeding processes. We recorded morphometric, behavioural (critical swimming speed, activity, aggressiveness, propensity to approach a novel object), and physiological parameters (plasma cortisol, glucose, ion concentrations, enzyme activity levels) after stress induction across four European perch stocks obtained from different aquaculture facilities in France (I and II), Denmark, and Hungary. The European perch stock from Denmark revealed the population with the most pronounced activity pattern. This was reflected by the highest relative swimming speed and a high percentage of bold-exploratory behaviour, which coincides with increased aggressive interactions within this stock. Additionally, we detected a higher tolerance to adverse environmental challenges in the perch stock from Denmark compared with the stocks from France and Hungary. The observed characteristics suggest that the stock from Denmark has a higher potential in the future framework of selective-breeding assessment. Further in-depth research is required to elucidate which traits and genetic as well as epigenetic components accelerate the domestication processes of European perch aquaculture and promote selective breeding processes.