Introduction Paediatricians, general practitioners (GPs) and midwives in primary care are important sources of information for parents on early childhood allergy prevention (ECAP). Research has shown that preventive counselling by health professionals can be effective in improving patients' health literacy (HL) and health behaviour. Providing effective advice relies on two factors. First, health professionals need be up-to-date with research evidence on ECAP, to consider popular misconceptions and fears and to translate this knowledge into clear recommendations for parents (knowledge translation). Second, they need to know and apply counselling techniques and create a practice setting which accommodates parental HL needs (health literacy-responsive care). The objective of this study is to explore and assess how German health professionals take up and translate ECAP evidence into appropriate recommendations for parents, how they consider HL in counselling and practice organisation and what barriers and enablers they find in their performance of HL-responsive ECAP. Methods and analysis The study has a sequential mixed-method design, in two phases. In the first phase, qualitative semi-structured expert interviews will be conducted with health professionals (paediatricians, GPs and midwives) at primary care level and professional policy level. Data collection is ongoing until January 2022. In the second phase, based on the qualitative results, a standardised questionnaire will be developed, and pilot-tested in a wider population of German health professionals. The findings of both phases will be integrated. Ethics and dissemination The study has received ethical approval from the Ethics Committee of the University of Regensburg (18-1205-101). The results will be published in international peer-reviewed open access journals and via presentations at scientific conferences. The results will also be shared with German health professionals, decision-makers and potential funders of interventions.