We present the updated photometric calibration of the twelve optical passbands for the Javalambre Photometric Local Universe Survey (J-PLUS) second data release (DR2), comprising 1088 pointings of two square degrees, and study the systematic impact of metallicity in the stellar locus technique. The [Fe/H] metallicity from LAMOST DR5 for 146184 high-quality calibration stars, defined with S/N > 10 in J-PLUS passbands and S/N > 3 in Gaia parallax, was used to compute the metallicity-dependent stellar locus (ZSL). The initial homogenization of J-PLUS photometry, performed with a unique stellar locus, was refined by including the metallicity effect in colours via the ZSL. The variation of the average metallicity along the Milky Way produces a systematic offset in J-PLUS calibration. This effect is well above 1% for the bluer passbands and amounts 0.07, 0.07, 0.05, 0.03, and 0.02 mag in u, J0378, J0395, J0410, and J0430, respectively. We modelled this effect with the Milky Way location of the J-PLUS pointing, providing also an updated calibration for those observations without LAMOST information. The estimated accuracy in the calibration after including the metallicity effect is at 1% level for the bluer J-PLUS passbands and below for the rest. We conclude that photometric calibration with the stellar locus technique is prone to significant systematic bias along the Milky Way location for passbands bluer than lambda = 4500 A. The updated calibration method for J-PLUS DR2 reaches 1-2% precision and 1% accuracy for twelve optical filters within an area of 2176 square degrees.
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