During the early phases of aerobic composting of animal manures, pathogens are inactivated primarily from the accumulation of heat produced by indigenous microbial activity. When compost materials are not exposed to these lethal temperatures, the required holding time needed to obtain a pathogen-free product that may be applied to fields is unknown. Consequently, a series of studies examined whether the carbon amendment (wheat straw, peanut hulls, rice hulls, and pine needles) added to animal manures affected survival of either Salmonella or E. coli O157:H7 during storage of compost mixtures at sublethal temperatures (20 to 40°C). Pathogens consistently survived for longer periods of time in compost mixtures prepared with pine needles than compost mixtures prepared with either of the other three carbon amendments. Pathogen inactivation in wheat straw- or peanut hull-amended compost mixtures was dependent on the target pathogen, moisture level, and storage temperature. Moisture levels in wheat straw-amended compost mixtures stored at 40°C had no effect on inactivation of E. coli O157:H7. In contrast, wheat straw-amended mixtures stored at 30 to 35°C and equilibrated to suboptimal moisture contents (30 to 40%) were less effective for inactivating pathogens compared with drier (25% moisture) or moister (60% moisture) mixtures. In peanut hull-amended compost mixtures, inactivation of E. coli O157:H7 was affected minimally by moisture levels, whereas Salmonella survival increased as the moisture level was decreased. The different inactivation responses of Salmonella and E. coli O157:H7 in compost mixtures prepared with wheat straw or peanut hulls and equilibrated to different moisture levels suggest that there are different mechanisms for inactivation. Hence, developing reliable guidelines relying on time-temperature for holding of compost mixtures at sublethal temperatures will be challenging and, perhaps, not possible.