The clinical features of COVID-19 and malaria are interrelated. Due to the similarity of symptoms between the two disease states, patients can be incorrectly diagnosed with the other ailment in areas with limited health resources. There is a dearth of knowledge of co-infection between COVID-19 and malaria from healthcare providers' perspective. Hence, this study assessed the ability of primary healthcare workers to diagnose malaria infection correctly from COVID-19 infection. A multistage sampling technique was used to select health care workers who were directly involved in malaria case management at 261 government-owned primary health facilities in Oyo State. Socio-demographic characteristics of respondents, knowledge and practices, COVID-19 differential diagnosis and challenges that healthcare workers face regarding malaria diagnosis were obtained using a standardized electronic structured questionnaire. Descriptive statistics, bivariate and multivariate analysis were conducted on data collected and significant results were interpreted at a 5% level of significance. A good percentage of the respondents (81.6%, 74.3%) had good knowledge about malaria and COVID-19. However, the knowledge gained did not translate to practice, as majority (86.2%) of respondents had poor malaria diagnosis practices. Practices relating to COVID-19 differential diagnosis in 69.7% of respondents were also poor. Most of the respondents attributed poor practices to the unavailability of Malaria Rapid Diagnostic Test (mRDT), inadequate training and continuous capacity improvement. Only 12.3% of the respondents have not had any form of training on malaria diagnosis and treatment in the last five years. Harmonization of regular trainings and continuous on-the job capacity building is essential to improve case identification, diagnosis and management of both ailments. Also, uninterrupted supplies of essential commodities such as mRDT in laboratories will reduce missed opportunities for malaria diagnosis.