Despite positive NCD policies in recent years, majority of Sub-Saharan African (SSA) health systems are inadequately prepared to deliver comprehensive first-line care for NCDs. Primary health care (PHC) settings in countries like Malawi and Zambia could be a doorway to effectively manage NCDs by moving away from delivering only episodic care to providing an integrated approach over time. As part of a collaborative health system strengthening project, we assessed and compared the preparedness and operational capacity of two target networks of public PHC settings in Lilongwe (Malawi) and Lusaka (Zambia) to integrate NCD services within routine service delivery. Data was collected and analyzed using validated health facility survey tools. These baseline assessments conducted between August 2018 and March 2019, also included interviews with 20 on-site health personnel and focal persons, who described existing barriers in delivering NCD services. In both countries, policy directives to decentralize disease-specific NCD services to the primary care level were initiated to meet increased demand but lacked operational guidance. In general, the assessed PHC sites were inadequately prepared to integrate NCDs into various service delivery domains, thus requiring further support. In spite of existing multi-faceted limitations, there was motivation among healthcare staff to provide NCD services.