Abstract Animal manures are a valued source of nutrients for crop production. They frequently do, however, contain zoonotic pathogens including a wide range of viruses. Ideally, manures would be treated prior to land application, reducing the burden of zoonotic viruses, and thus the potential for transmission to adjacent water resources or crops intended for human or animal consumption. In the present study, manure was obtained from four dairy and three swine farms. The manure was incubated anaerobically in the laboratory for 28 weeks at temperatures ranging from 4 to 25 °C, and multiple physical and chemical parameters were monitored. The abundance of various DNA and RNA viruses was measured throughout the incubation by amplifying virus-specific gene targets. A combination of statistical analyses were applied to identify whether the viruses are significantly impacted by temperature transition or affected by other abiotic factors. Temperature had no effect on the persistence of any of the viruses studied. An increase in pH of the manures during the incubation was significantly (P < 0.05) associated with decreased persistence, suggesting that pH manipulation during storage could reduce the abundance of viruses. Graphical abstract Unlabelled Image Highlights • Detection and quantification of DNA and RNA viruses in swine and dairy manures. • Temperature transitions had a negligible effect on manure characteristics and virus persistence. • Persistence and survival in swine and dairy cow manures were virus dependent. • The pH was the main abiotic factor modifying physical and chemical characteristics of manures. • Alkalinity showed a strong detrimental effect on virus persistence in manure. [ABSTRACT FROM AUTHOR]