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This study presents the properties of a new group of ionic liquids (ILs) based on various cations and pelargonic acid, a natural nonselective herbicide. The obtained bio-ILs were obtained with high yield (>92%) using a metathesis reaction or neutralization of quaternary ammonium hydroxides and characterized in terms of physicochemical properties. Tests under greenhouse conditions confirmed the superior herbicidal activity of ILs compared to pure pelargonic acid, especially against white mustard (5–10-fold higher efficacy of ILs). Further studies under field conditions revealed that tetrabutylammonium, benzalkonium, and oleyltrimethylammonium pelargonates exhibited the highest efficiency (50.5%, 49.5%, and 46.7%, respectively) at an approximately 3-fold lower dose of pelargonic acid (2.72 kg per 1 ha) compared to that used in commercial products (8–11 kg per 1 ha). This allows classification of the synthesized ILs as bioherbicidal ionic liquids (bio-HILs). In addition to bio-HILs, two new auxins were also obtained. Evaluation of antimicrobial activity indicated that the most potent effect was observed in the case of salts with oleyltrimethylammonium and tallowtrimethylammonium cations [minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and minimum fungicidal concentration (MFC) values lower by 2 orders of magnitude compared to pelargonic acid]. The fundamental influence of the cation was also observed during biodegradability assay, as the results varied from 0% to 85% (the highest biodegradability was observed in the case of dodecylbetainium and tetrabutylammonium pelargonates). The computational data suggested that biodegradation efficiency seems to be influenced by the interactions between the cation and the anion. The performed toxicity tests allowed classification of the obtained bio-HILs as category V [di­(hydrogenated tallow)­dimethylammonium pelargonate] or category IV compounds against rats.