Fatty acids are long-chain carboxylic acids that readily produce [M – H]– ions upon negative ion electrospray ionization (ESI) and cationic complexes with alkali, alkaline earth, and transition metals in positive ion ESI. In contrast, only one anionic monomeric fatty acid–metal ion complex has been reported in the literature, namely [M – 2H + FeIICl]–. In this manuscript, we present two methods to form anionic unsaturated fatty acid–sodium ion complexes (i.e., [M – 2H + Na]–). We find that these ions may be generated efficiently by two distinct methods: (1) negative ion ESI of a methanolic solution containing the fatty acid and sodium fluoride forming an [M – H + NaF]– ion. Subsequent collision-induced dissociation (CID) results in the desired [M – 2H + Na]– ion via the neutral loss of HF. (2) Direct formation of the [M – 2H + Na]– ion by negative ion ESI of a methanolic solution containing the fatty acid and sodium hydroxide or bicarbonate. In addition to deprotonation of the carboxylic acid moiety, formation of [M – 2H + Na]– ions requires the removal of a proton from the fatty acid acyl chain. We propose that this deprotonation occurs at the bis-allylic position(s) of polyunsaturated fatty acids resulting in the formation of a resonance-stabilized carbanion. This proposal is supported by ab initio calculations, which reveal that removal of a proton from the bis-allylic position, followed by neutral loss of HX (where X = F– and –OH), is the lowest energy dissociation pathway.