Despite growing calls for the explicit application of theory when designing behaviour change interventions, limited empirical evidence exists regarding the effectiveness of these methods compared to non-theoretical approaches. A cluster randomized controlled trial (Hide and Seek Project - HaSP) tested two implementation approaches for improving hereditary cancer referral practices with one key distinction: implementation strategies were designed based explicitly on psychological theory, or based on stakeholder intuition. This study presents the detailed methods and resources used to facilitate this comparison, whilst examining the strategies generated through both approaches. Across seven Australian hospitals, clinical stakeholders attended focus-groups to co-design site-specific strategies for improving Lynch syndrome referral. Co-design methods differed according to trial arm. Implementation strategy content was examined, with intuitively-derived strategies retrospectively coded to determine theoretical alignment. Fifty-one strategies were proposed across all sites (theory-based arm = 32, intuition-based arm = 19). Overall, nine Behaviour Change Technique (BCT) categories were used on 77 occasions. In the theory-based trial arm, eight BCT categories were identified on 53 occasions; versus five BCT categories on 24 occasions in the intuition-based arm. BCT categories were largely similar across both arms. After retrospectively coding intuitively-derived strategies, 42% contained mechanistic links, thereby demonstrating theoretical alignment. Methods facilitated robust comparison of theoretical and intuitive approaches to implementation strategy design. Recognising the known benefits of theory for enhancing scientific learning, applying these methods on a larger scale may provide definitive evidence about the comparative effectiveness of theoretical approaches.