Measuring and modelling manure temperatures are crucial for estimating greenhouse gas emissions from liquid manure storage. The manure temperature was recorded at various depths in two swine slurry storage tanks situated in Vallentuna (VA) and Örsundsbro (OR) in Sweden. These data were used to assess the effectiveness of a revised mechanistic model for estimating manure temperatures, which incorporates the effects of wall shading, snow cover, and manure input mixing. The average manure temperatures were higher than air temperatures in the summer and fall. This indicated that using air temperature would result in an underestimation of methane emissions when applying the 2019 IPCC Refinement methodology. The revised model estimated manure temperatures for spring, summer, fall, and winter as 4.8, 16.1, 7.8, and 2.6 °C at the VA tank and 11.6, 17.1, 9.5, and 3.6 °C at the OR tank. The root mean square errors between daily simulated and observed temperatures in the summer decreased in both tanks due to incorporating shadow effect into the revised model. Fall estimates did not improve, possibly because of uncertainties from slurry removal and higher precipitation inputs. Sensitivity analysis indicated that solar radiative heat input was reduced with higher tank walls and smaller tank diameters when applying the revised model. Wall shading may influence manure temperatures in tanks with small diameters at high-latitude locations. This study offers insights into understanding the relationship between manure temperatures and its thermal balance influenced by latitude, storage design, snow cover and mixing, and its implications for accurately estimating methane emissions.