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Abstract Background As integrated care systems are embedded across England there are regions where the integration process has been evaluated and continues to evolve. Evaluation of these integrated systems contributes to our understanding of the challenges and facilitators to this ongoing process. This can support integrated care systems nationwide as they continue to develop. We describe how two integrated care partnerships in different localities, at differing stages of integration with contrasting approaches experienced challenges specifically when integrating with primary care services. The aim of this analysis was to focus on primary care services and how their existing structures impacted on the development of integrated care systems. Methods We carried out an exploratory approach to re-analysing our previously conducted 51 interviews as part of our prior evaluations of integrated health and care services which included primary care services. The interview data were thematically analysed, focussing on the role and engagement of primary care services with the integrated care systems in these two localities. Results Four key themes from the data are discussed: (i) Workforce engagement (engagement with integration), (ii) Organisational communication (information sharing), (iii) Financial issues, (iv) Managerial information systems (data sharing, IT systems and quality improvement data). We report on the challenges of ensuring the workforce feel engaged and informed. Communication is a factor in workforce relationships and trust which impacts on the success of integrated working. Financial issues highlight the conflict between budget decisions made by the integrated care systems when primary care services are set up as individual businesses. The incompatibility of information technology systems hinders integration of care systems with primary care. Conclusions Integrated care systems are national policy. Their alignment with primary care services, long considered to be the cornerstone of the NHS, is more crucial than ever. The two localities we evaluated as integration developed both described different challenges and facilitators between primary care and integrated care systems. Differences between the two localities allow us to explore where progress has been made and why.