Background: Isoniazid is a leading tuberculosis treating medication. Global supply chains provide essential medicines such as isoniazid to resource-limited areas. Ensuring the safety and efficaciousness of these medicines is essential to public health programs. Handheld spectrometers are becoming increasingly approachable in cost and usability. As supply chains expand, quality compliance screening of essential medications is necessary in site-specific locations. Here, a brand-specific qualitative discrimination analysis of isoniazid is approached by collecting data from two handheld spectrometers in two countries with the intent to build a multi-location quality compliance screening method for a brand of isoniazid. Methods: Two handheld spectrometers (900–1700 nm) were used to collect spectra from five manufacturing sources (N = 482) in Durham, North Carolina, USA, and Centurion, South Africa. A qualitative brand differentiation method was established from both locations by applying a Mahalanobis distance thresholding method as a measure of assessing similarity. Results: Combining data from both locations resulted in a 100% classification accuracy, at both locations, for brand ‘A’ and resulted in the four other brands classifying as dissimilar. Bias was found between sensors in terms of resulting Mahalanobis distances, but the classification method proved to be robust enough to accommodate. Several spectral peaks found in isoniazid references appear within the 900–1700 nm range, as well as variation in the excipients per manufacturer. Conclusions: Results show promise for compliance screening isoniazid as well as other tablets in multiple geographic locations using handheld spectrometers.