Background: Long lasting insecticidal nets (LLIN) are a key vector control tool used for the prevention of malaria. Active ingredient (AI) measurements in LLIN are essential for evaluating their quality and effectiveness. The main aim of the present study was to determine the utility of X-ray fluorescence (XRF) spectroscopy as a suitable in-field tool for total AI quantification in LLINs. Methods: New and unused LLIN samples containing deltamethrin (PermaNet 2.0, n = 35) and alpha-cypermethrin (SafeNet, n = 43) were obtained from batches delivered to PNG for mass distribution. Insecticides were extracted from the LLINs using a simple extraction technique and quantified using liquid chromatography mass spectrometry (LC-MS). The LC-MS results were correlated with in-field XRF spectroscopy measurements on the same nets. Operators were blinded towards the identity of the nets. Bioefficacy of the LLIN samples was tested using WHO cone bioassays and test results were correlated with total AI content. Results: The results indicate a close agreement between the quantitative XRF and LC-MS. Interestingly, the total AI content was negatively correlated with bioefficacy in PermaNet 2.0 (especially, in recently manufactured nets). In contrast, AI content was positively correlated with bioefficacy in SafeNet These results indicate that the chemical content analysis in predelivery inspections does not always predict bioefficacy well. Conclusion: XRF is a promising in-field method for quantification of both deltamethrin and alpha-cypermethrin coated LLINs. Since total AI content is not always a predictor of the efficacy of LLIN to kill mosquitoes, bioefficacy measurements should be included in predelivery inspections.