Unprovenanced skeletal remains housed in anatomy laboratories, medical schools, and museums present a persistent ethical challenge when the human skeletal remains potentially represent historically marginalized or legally protected populations. Reliance on a single line of evidence, like epitaphonomic indicators or population affinity estimates, may result in incomplete or misleading assessments. Herein, we present a structured, non-destructive protocol integrating epitaphonomic signatures and an estimation of population affinity (including assessing biocultural indicators of affinity) to support ethical decision-making regarding unprovenanced crania in institutional collections. Our proposed protocol was applied to 16 unprovenanced crania curated in a university anatomy collection. Epitaphonomic signatures associated with anatomical preparation were assessed using categorical scores; craniometric data were analyzed using FORDISC 3.1 following the standard approach therein and using a custom reference dataset imported into the program. Additional exploratory analyses were conducted using a Factor Analysis of Mixed Data (FAMD) to visualize concordance and discordance between epitaphonomic and craniometric variables. Results indicate most individuals exhibit epitaphonomic signatures consistent with anatomical preparation; however, when those data are integrated with craniometric analysis, we identified individuals warranting removal from teaching collections based on elevated ethical concerns. Case examples demonstrate how our protocol supports transparent ethical triage distinguishing between likely anatomically prepared human remains, human remains requiring repatriation, and indeterminate cases requiring further evaluation. This protocol provides a practical, nondestructive framework for the responsible stewardship of unprovenanced skeletal collections.