This paper describes a two-step method to prepare novel copper-methanol nanofluids capped with a short chain molecule, (3-Aminopropyl)trimethoxysilane (APTMS). Two commercial nanopowders were dispersed at various powers using a 20 kHz ultrasonic probe into solutions of methanol and the capping agent. Ultrasonic energy input was measured by calorimetry with z-average diameters, intensity and number size distributions recorded by a dynamic light scattering technique. The stability of the dispersion was monitored visually, and quantified by recording the zeta potential. Dispersions of the bare powder were used as a control. Absorption spectroscopy was used to confirm the presence of the capping agent. The thermal conductivities of 0 to 10% wt./vol. (1.1% vol.) dispersions of the capped copper-methanol nanofluid were determined using a C-Therm analyzer. Optimum ultrasonic de-agglomeration conditions gave dispersions with a z-average particle size of <200 nm and a PdI of <0.2. The capped particles showed good stability; up to six months in some instances, and an average zeta potential of +38 mV was recorded. The thermal conductivity of the nanofluid increased with concentration, and an enhancement of 9% over the base fluid was found at 10% wt./vol. (1.1% vol.). This innovative work has demonstrated the ultrasonic preparation and stability of copper nanoparticles protected with APTMS; a short chain molecule which binds to copper and prevents oxidation. The protected particles can enhance the thermal conductivity of methanol with no interference from the capping ligand.