Nanoscale devices with Terahertz (THz) communication capabilities are envisioned to be deployed within human bloodstreams. Such devices will enable fine-grained sensing-based applications for detecting early indications (i.e., biomarkers) of various health conditions, as well as actuation-based ones such as targeted drug delivery. Associating the locations of such events with the events themselves would provide an additional utility for precision diagnostics and treatment. This vision yielded a new class of in-body localization coined under the term “flow-guided nanoscale localization”. Such localization can be piggybacked on THz communication for detecting body regions in which biological events were localized with the traveling time reported by nanodevices flowing with the bloodstream. From decades of research on objective benchmarking of “traditional” indoor localization and its eventual standardization (e.g., ISO/IEC18305:2016), we know that in early stages, the reported performance results were often incomplete (e.g., targeting a subset of relevant performance metrics). Reported results in the literature carried out benchmarking experiments in different evaluation environments and scenarios and utilized inconsistent performance indicators. To avoid such a “lock-in” in flowguided localization, we propose a workflow for standardized performance evaluation of such approaches. The workflow is implemented in the form of an open-source simulation framework that is able to jointly account for the mobility of the nanodevices, in-body THz communication with on-body anchors, and energy-related and other technological constraints (e.g., pulsebased modulation) at the nanodevice level. Accounting for these constraints, the framework can generate raw data to streamline into different flow-guided localization solutions for generating standardized performance benchmarks.