Background: Studies examining psychosocial and depression assessment programs in maternity settings have not adequately considered the context in which psychosocial assessment occurs or how broader components of integrated care, including clinician decision-making aids, may optimise program delivery and its cost-effectiveness. There is also limited evidence relating to the diagnostic accuracy of symptom-based screening measures used in this context. The Perinatal Integrated Psychosocial Assessment (PIPA) Project was developed to address these knowledge gaps. The primary aims of the PIPA Project are to examine the clinical- and cost-effectiveness of two alternative models of integrated psychosocial care during pregnancy: 'care as usual' (the SAFE START model) and an alternative model (the PIPA model). The acceptability and perceived benefit of each model of care from the perspective of both pregnant women and their healthcare providers will also be assessed. Our secondary aim is to examine the psychometric properties of a number of symptom-based screening tools for depression and anxiety when used in pregnancy. Methods: This is a comparative-effectiveness study comparing 'care as usual' to an alternative model sequentially over two 12-month periods. Data will be collected from women at Time 1 (initial antenatal psychosocial assessment), Time 2 (2-weeks after Time 1) and from clinicians at Time 3 for each condition. Primary aims will be evaluated using a between-groups design, and the secondary aim using a within group design. Discussion: The PIPA Project will provide evidence relating to the clinical- and cost- effectiveness of psychosocial assessment integrated with electronic clinician decision making prompts, and referral options that are tailored to the woman's psychosocial risk, in the maternity care setting. It will also address research recommendations from the Australian (2011) and NICE (2015) Clinical Practice Guidelines.