•Application of ID-LC/MS/MS for the accurate determination of vitamin K1 isomers.•Quantification of trans- and cis-vitamin K1 in the primary reference material by NMR.•Minimization of the measurement bias using APCI rather than ESI.•Developed method was proven to have high-order metrological quality. A method based on isotope dilution-liquid chromatography/tandem mass spectrometry (ID-LC/MS/MS) using a C30 column has been developed for the separate and accurate determination of trans- and cis-vitamin K1 in infant formula. Vitamin K1 and the deuterium-labeled internal standard eluted at slightly different retention times experiencing different matrix effects, and this possibly resulted in biased measurement. The matrix effect profiles obtained from post-column infusion experiments showed that atmospheric pressure chemical ionization (APCI) was less susceptible to matrix effects near the retention time than electrospray ionization (ESI); therefore, APCI was used in this study. The developed method was validated by measuring fortified samples, and the results agreed with the gravimetric values. Its repeatability and reproducibly were within 2% relative standard deviation. The relative expanded uncertainty was approximately 5%, indicating that the method was of higher-order metrological quality as a reference method.