Polar metal–organic frameworks have potential applications as functional non-linear optical, piezoelectric, pyroelectric and ferroelectric materials. Using second harmonic generation microscopy we found that fluoride doping of the microporous iron(III) terephthalate MOF MIL-53(Fe) induces a polar organization in its structure, which was not previously detected with XRD. The polar order is only observed when both fluoride and guest molecules are present, and may be related to a complex interplay between the adsorbates and the framework, leading to a modification of the positioning of fluoride in the inorganic Fe-chains. Combined polarized second harmonic generation microscopy and scanning pyroelectric microscopy show that the polar axis is unidirectional and of the same sense over the whole crystal, extending up to 100 micrometers. This finding shows how MOF materials can be endowed with useful properties by doping MOFs with fluoride.