Elemental analysis of calcium (Ca) and phosphorus (P) has been shown to be useful in differentiating skeletal and nonskeletal material. X‐ray fluorescence spectrometry (XRF) is an attractive, nondestructive technique for forensic anthropologists, and the development of portable XRF instrumentation is promising for field applications. This study examines the performance of handheld XRF instrumentation operated in air compared to a traditional benchtop XRF device that has the ability to control the analysis atmosphere. Both instruments can be used to effectively distinguish skeletal from nonskeletal remains. However, as the measurement atmosphere affects detection levels for calcium and phosphorus, Ca/P ratios obtained from the instruments and analysis conditions were found to differ significantly, with analyses conducted in air showing significantly lower phosphorus detection. Consequently, comparison of Ca/P ratios to conclude skeletal versus nonskeletal origin must be based on data collected under similar analysis conditions.