Thousands of Marine Protected Areas (MPAs) have been designated around the globe to conserve benthic habitats, following the adoption of Convention on Biodiversity Aichi Target 11 and widespread endorsement of the ‘30by30’ initiative. When designed and managed effectively, MPAs can enrich biodiversity, enhance ecosystem services and regulate stakeholder access. High quality dedicated monitoring programmes are essential to determine MPA effectiveness at the correct spatial and temporal scales; however, such programmes can be fraught with complexities and many MPAs have not yet implemented them following designation. There is, therefore, a clear need and opportunity for scientists to share and draw on collective experiences to help reduce barriers to successful MPA monitoring. This study synthesises lessons learned and challenges encountered in the English MPA monitoring programme, reflecting on solutions and future directions. Twenty-three MPA monitoring reports were reviewed and the key findings were extracted. The majority were centred around the need to consider monitoring approaches at the scale of each individual MPA, rather than adoption of generic ‘one-size-fits-all’ practices. Various challenges were found to be inherent, whilst some were prioritised for further development: MPA-scale measures of condition, fishing activity data, seabed imagery acquisition and analysis, DNA technologies, habitat mapping, and ecosystem approaches to MPA monitoring. This study highlights the benefits of strong multi-disciplinary partnerships for addressing the complex issues encountered in MPA monitoring programmes. We endorse further studies, technical advancements and a more holistic ecosystem approach to understanding human impacts on the benthos, thus optimising MPA management and positive conservation outcomes.