Egg incubation of mule ducks, mainly used for fatty liver production, is one of the critical phases in this sector. Based on hatching rate, the best incubation parameters have already been well described for poultry, but the literature on ducks is lacking. In this study, we tested different incubation conditions by varying two important factors, temperature and relative humidity, in mule ducks. These variations were applied at different periods during embryogenesis in order to measure the impact of environmental disturbances on different zootechnical performances. The temperature was increased by 1.5 °C (16 h/24) and the relative humidity was set up to 65%, during 10 days. Six 10-day developmental windows were tested, from embryonic day 9 to embryonic day 14. Our results are in line with previous reports showing that increasing incubation temperature, even when relative humidity is adjusted, can have a negative impact on duck embryonic mortality up to 24.5% for the condition E10-E20 (P < 10−5). However, the hatchability can be maintained at the level of the control groups when these modifications are applied on the latest windows (from the 11th embryonic day). Sex ratio, hatching BW, and internal temperature are also sensitive to these incubation changes, and their modification could have a major impact on later zootechnical performance. These results should contribute to the development or embryonic temperature programming approaches, especially for the fatty liver production industry