Medical educators are tasked with decisions on trainee progression and credentialing for independent clinical practice, which requires robust evidence from workplace-based assessment. It is unclear how the current promotion of workplace-based assessment as a pedagogical approach to promote learning has impacted this use of assessments for decision-making; meeting both these purposes may present unforeseen challenges. In this study we explored how supervisors make decisions on trainee progress in practice. We conducted semi-structured interviews with 19 supervisors of postgraduate anesthesia training across Australia and New Zealand and undertook thematic analysis of the transcripts. Supervisors looked beyond the formal assessment portfolio when making performance decisions. They instead used assessment 'shadow systems' based on their own observation and confidential judgements from trusted colleagues. Supervisors' decision making involved expert judgement of the perceived salient aspects of performance and the standard to be attained while making allowances for the opportunities and constraints of the local learning environment. Supervisors found making progress decisions an emotional burden. When faced with difficult decisions, they found ways to share the responsibility and balance the potential consequences for the trainee with the need to protect their patients. Viewed through the lens of community of practice theory, the development of assessment 'shadow systems' indicates a lack of alignment between local workplace assessment practices and the prescribed programmatic assessment approach to high-stakes progress decisions. Avenues for improvement include cooperative development of formal assessment processes to better meet local needs or incorporating the information in 'shadow systems' into formal assessment processes.