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The conversion of organic waste streams into carboxylic acids as renewable feedstocks results in relatively dilute aqueous streams. Carboxylic acids can be recovered from such streams by using liquid–liquid extraction. Hydrophobic ionic liquids (ILs) are novel extractants that can be used for carboxylic acid recovery. To integrate these ILs as in situ extractants in several biotechnological applications, the IL must be compatible with the bioprocesses. Herein the ILs [P666,14][oleate] and [N8888][oleate] were synthesized in water and their bioprocess compatibility was assessed by temporary exposure to an aqueous phase that contained methanogenic granular sludge. After transfer of the sludge into fresh medium, [P666,14][oleate]‐exposed granules were completely inhibited. Granules exposed to [N8888][oleate] sustained anaerobic digestion activity, albeit moderately reduced. The IL contaminants, bromide (5–500 ppm) and oleate (10–4000 ppm), were shown not to inhibit the methanogenic conversion of acetate. [P666,14] was identified as a bioprocess‐incompatible component. However, our results showed that [N8888][oleate] was bioprocess compatible and, therefore, has potential applications in bioprocesses.

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