Most farm assurance schemes in the UK at least, in part, aim to provide assurances to consumers and retailers of compliance with welfare standards. Inclusion of welfare outcome assessments into the relevant inspection procedures provides a mechanism to improve animal welfare within assurance schemes. In this study, taking laying hens as an example, we describe a process for dealing with the practical difficulties in achieving this in two UK schemes; Freedom Food and Soil Association. The key challenges arise from selecting the most appropriate measures, defining sampling strategies that are feasible and robust, ensuring assessors can deliver a consistent evaluation and establishing a mechanism to achieve positive change. After a consultation exercise and pilot study, five measures (feather cover, cleanliness, aggressive behaviour, management of sick or injured birds, and beak trimming) were included within the inspection procedures of the schemes. The chosen sampling strategy of assessing 50 birds without handling provided reasonable certainty at a scheme level but less certainty at an individual farm level. Despite the inherent limitations within a time and cost sensitive certification assessment, the approach adopted does provide a foundation for welfare improvement by being able to highlight areas of concern requiring attention, enabling schemes to promote the use of outcome scoring as a management tool, promoting the dissemination of relevant technical information in a timely manner and increasing the scrutiny of standards important for the welfare of the birds.