•Coinfection of cassava with Cassava brown streak disease virus and its Ugandan variant is a threat to cassava production.•Coinfection is highly sensitive to roguing frequency and vector mortality.•Temperature variability causes multiple seasonal whitefly generations resulting in multiple epidemics.•Management of nymph development is more important than whitefly fecundity rate for epidemics’ control. Mixed infections of Cassava brown streak virus (CBSV) and its Ugandan variant (UCBSV) in cassava hosts are increasingly threatening food security in East and Central Africa. The possibility of these viruses spreading to cassava producing countries in West Africa is of great concern. Most epidemiological models developed to address this challenge do not include the possibility of coinfection and whitefly lifecycle in managing these viruses. The question is: how does the inclusion of whitefly lifecycle and temperature variability influence disease outbreak and spread? We develop a host-vector-virus coinfection model that incorporates the whitefly life cycle and temperature variability as drivers of an epidemic. Using a combination of analytical and numerical simulations, we identify the key factors that drive disease outbreaks in cassava plantations. We also demonstrate that management of the whitefly's immature development stage can reduce disease prevalence and crop losses associated with these outbreaks. These results suggest that biological control agents using natural enemies should be given higher priority than the use of insecticides in management strategies.