Researchers are increasingly engaged in studies to determine and correct negative welfare consequences of animal husbandry and behaviour modification procedures, not least in response to industries’ growing need to maintain their social licence through demonstrable welfare standards that address public expectations. To ensure that welfare recommendations are scientifically credible, the studies must be rigorously designed and conducted, and the data produced must be interpreted with full regard to conceptual, methodological, and experimental design limitations. This commentary provides guidance on these matters. In addition to, and complementary with, the ARRIVE guidelines that deal with animal studies in general, there is a need for additional specific advice on the design of studies directed at procedures that alter behaviour, whether through training, handling, or restraint. The COMPASS Guidelines offer clear direction for conducting welfare-focused behaviour modification research. They stand for the following: Controls and Calibration, emphasising rigorous design, baseline measures, equipment calibration, and replicability; Objectivity and Open data, ensuring transparency, validated tools, and data accessibility; Motivation and Methods, with a focus on learning theory, behavioural science, and evidence-based application of positive reinforcers and aversive stimuli; Precautions and Protocols, embedding the precautionary principle, minimising welfare harms, listing stop criteria, and using real-time monitoring; Animal-centred Assessment, with multimodal welfare evaluation, using physiological, behavioural, functional, and objective indicators; Study ethics and Standards, noting the 3Rs (replacement, reduction, and refinement), welfare endpoints, long-term effects, industry independence, and risk–benefit analysis; and Species-relevance and Scientific rigour, facilitating cross-species applicability with real-world relevance and robust methodology. To describe these guidelines, the current article is organised into seven major sections that outline detailed, point-by-point considerations for ethical and scientifically rigorous design. It concludes with a call for continuous improvement and collaboration. A major purpose is to assist animal ethics committees when considering the design of experiments. It is also anticipated that these Guidelines will assist reviewers and editorial teams in triaging manuscripts that report studies in this context.