When excavating complex anthropogenic stratigraphies, the field archaeologist is often limited to prioritizing the sampling strategy based on in situ macroscopic interpretations. Not until months after the excavation do supporting information and interpretations such as micromorphological analysis offer a more nuanced picture. This article addresses this challenge by evaluating two methods for analyzing results as the excavation is ongoing: computer tomography (CT) and cone beam CT-scanning (CBCT-scanning) of soil blocks using commercially available medical scanners (0.6 mm and 0.3 mm resolution) and an impregnation and micromorphological sediment screening (MSS) approach. The combined methods were applied on samples from a Neolithic settlement (n = 24), an Iron Age / Viking Age cult (n = 9), and an Iron Age settlement (n = 1) in Denmark. Results showed that the CBCT-scanning did not offer clear visual documentation of the different densities between, for example, organic-rich and sandy layers, while the micromorphological screening showed potential when a fluorescent agent (Epodye) was added to the epoxy. Hence, the results suggest that the epoxy impregnation makes it possible to detect microstratigraphical features, while further identification requires a traditional micromorphological thin-section analysis. It would require a larger quantity of samples to assess the procedure’s cost-efficiency on a larger scale.