The endohedral fullerene molecule, N@C60, is a candidate for molecular spin qubits (quantum bits) and spin probes owing to its exceptional electron spin properties. Advancements in the processing of N@C60 are key to obtaining samples of high purity on a reasonable timescale. We investigate enrichment by high throughput processing (flow rate of 18 L h−1 and operating pressure of 1.5–2 MPa) using high performance liquid chromatography (HPLC) as a means of scaling N@C60 production. We use detection by electron paramagnetic resonance (EPR) spectroscopy to map N@C60 during processing, and through the reconstruction of the peak position in the chromatogram, we are able to determine the retention time and relative purity of N@C60 without the need for its isolation. Based on this, we establish a procedure for time-efficient, high throughput processing to isolate N@C60 in high purity.