We demonstrate the first use of Resonant Acoustic Mixing (RAM) without bulk solvent for the synthesis of short oligonucleotide fragments. Using the modified H-phosphonate approach, DNA, RNA, and 2′-modified nucleotides were successfully coupled to 3′-protected nucleosides in high yields (63–92%) while reducing solvent volume by 90%. In addition to synthesizing protected phosphodiester (PO) dimers and trimers, we also synthesized protected phosphorothioate (PS) dimers in good yields (63–65%). Using phosphoramidite chemistry, we were similarly able to reduce the solvent volume by 90% while coupling DNA phosphoramidites (58–92%) and RNA phosphoramidites (55–95%) with 3′-protected nucleosides in high yields followed by traditional oxidation with iodine in solution. Both strategies were successfully scaled up to multi-gram quantities which was facilitated by the use of RAM, offering the potential for larger scale-up, up to hundreds of kilograms continuously.