Uncertainty in estimates of elastic properties of soft mudrock components, such as clay minerals and kerogen, can influence well-log-based evaluation of effective elastic properties in organic-rich mudrocks. Existing methods, such as effective medium models for well-log-based assessment of elastic properties, assume a constant stiffness and an idealized shape for rock components. However, these characteristics might vary depending on the distribution and size of that particular component, as well as its adjacent components. Furthermore, there is a significant uncertainty in elastic properties of kerogen in the case of organic-rich mudrocks. The uncertainty associated with the aforementioned parameters on effective elastic properties of rocks has not been investigated in existing publications. In this paper, we quantified the variability in elastic properties of individual mudrock components caused by their spatial distribution, size, and rock fabric at the microscale and their impacts on well-log-based evaluation of effective elastic properties. We performed nanoindentation mechanical tests on samples from the Haynesville and the lower Eagle Ford Formations, to measure Young’s modulus and hardness at targeted locations. Then, we quantified the variability of Young’s modulus in the microscale and its impact on effective elastic properties at the micro- and well-log scales. Results reveal significant uncertainties in measurements of elastic properties of soft rock components, associated with their location and size. Young’s moduli of individual clay components are higher when located adjacent to stiff rock components, such as large quartz and calcite grains. Results reveal that 25% and 12% uncertainties in measured elastic properties of clay minerals affect well-log-based estimates of effective elastic stiffness coefficients up to 29% and 11% in the Haynesville and the lower Eagle Ford Formations, respectively. These uncertainties can be more significant in cases with a higher concentration of clay minerals and kerogen.