4-Amino-4-deoxy-L-arabinopyranose (Ara4N) residues have been linked to antibiotic resistance by reducing the negative charge in the lipid A and core region of the bacterial lipopolysaccharide (LPS). To study the enzymatic transfer of Ara4N onto lipid A, which is catalysed by the ArnT transferase, we chemically synthesised a series of anomeric phosphodiester linked lipid Ara4N derivatives containing linear aliphatic chains as well as E- and Z-configured monoterpene units. Coupling reactions were based on sugar-derived H-phosphonates, followed by oxidation and global deprotection. The enzymatic Ara4N transfer was performed in vitro with crude membranes from a deep-rough mutant from Escherichia coli as acceptor. Product formation was detected by TLC and LC-ESI-QTOF mass spectrometry. Out of seven analogues tested, only the -neryl derivative was accepted by the Burkholderia cenocepacia ArnT protein leading to substitution of the Kdo2-lipid A acceptor, thus providing evidence that ArnT is an inverting glycosyl transferase that requires the Z-configured double bond next to the anomeric phosphate. This approach provides an easily accessible donor substrate for biochemical studies concerning modifications of bacterial LPS that modulate antibiotic resistance and immune recognition.