This paper reports the use of an immobilised ruthenium complex in a continuous flow process for the N-alkylation of morpholine with benzyl alcohol. The ruthenium-based catalyst was supported on a phosphine bound polymer. Screening experiments were first performed in a batch reactor, with a 16vol% mixture of morpholine and benzyl alcohol (stoichiometric molar ratio of 1:1) in toluene as the solvent. Operating at 110°C for 24h, it was shown that high conversions (>99%) into the desired tertiary amine could be achieved. This reaction was then shown to be viable in a continuous flow reactor, where the catalytic polymer beads were retained in the bed. Operating at 150°C and using p-xylene as a solvent, the conversion into the desired tertiary amine was shown to be as high as 98%. This approach is clearly very promising, as it provides a greener and more atom efficient route for the production of secondary and tertiary amines in the pharmaceutical industry.