Laboratory-based decay experiments have become commonly used to supplement our understanding of how organisms enter the fossil record. Differences in how these experiments are designed and evaluated, however, including dissimilarities in qualitative decay-scoring indices superimposed on variability in model organisms, renders any semblance of comparison between studies unreliable. Here, we introduce the utility of X-ray tomographic microscopy (μCT) as a means for reliable and repeatable analysis of soft-tissue decay experiment products. As proof-of-concept, we used a relatively simple experimental design with classic studies as comparators, and present our analytical protocol using μCT for capturing the entire volume of the decay subject. Segmentation software then allows for 3D volume analysis and high-resolution internal and external character identification. We describe the workflow from sample preparation, contrast-staining, and data collection to processing and analysis of the resulting data, using peppermint shrimp (Lysmata wurdemanni) as model organisms, and compare our results to previous taphonomic studies. These methods allow for improved visualization and quantification of decay and internal volume analysis with minimal handling as compared to traditional qualitative scoring methods. Using the same scoring criteria as previous studies, this study revealed similar decay results for certain features, while we were additionally able to detect other feature loss or alteration earlier—importantly without need for potentially distortive sample handling. We conclude that μCT is a more effective, straightforward, and exact means for extracting quantitative data on the progression of decay and should be adopted in future studies, where available, to streamline and standardize comparisons.