Longitudinal birth cohort research provides a glimpse into the biological and social trajectories of a cohort of people, which helps us to better understand how to improve health and social outcomes. While qualitative longitudinal, ethnographic, and other qualitative research methods are increasingly used to capture complex data in trials and cohort research, they are relatively less common, and they vary greatly within and across cohorts and national contexts. The aim of this scoping review is to provide an overview of the use of qualitative and innovative methods in longitudinal preconception and birth cohort studies. Innovative methods, defined by Mannell and Davis (2019), go beyond standard surveys, interviews, and focus groups. The review summarises the literature of the integration of qualitative methods into birth cohort methodologies. Five databases were searched systematically, using MeSH and free text terms, for articles published in English before October 2022. Two-thirds of titles, abstracts, and full-text papers were screened by independent reviewers. Data extraction followed the Centre for Reviews and Dissemination guidelines and was based on features of qualitative methods from the COREQ checklist. 43 papers were included from the 13909 papers identified from the database search. The majority of the birth cohort studies used ‘traditional qualitative methods’ such as focus groups and one-to-one interviews. The studies that used ‘innovative qualitative methods’ included participatory interviews with photovoice, photographs, and using scenario and story cards, and while not a steadfast requirement of innovation, often included coproduction between the researchers and the participants. Although the literature reports challenges in conducting innovative methods within birth studies such as time and power imbalances between researcher and participant, these methods can help us better understand how to improve social and health outcomes.