Beta-cyclodextrin (β-CD) inclusion complexes with naturally derived antimicrobial (AM) agents: thymol, carvacrol and linalool were prepared using a co-precipitation technique. Conditions including solvent composition, temperature, reaction time and total solvent volume were investigated to optimise the inclusion efficiency (IE) and yield. Electrospray ionisation mass spectrometry was used to confirm the formation of the thymol/β-CD complex and gas chromatography was used to quantify the amount AM agent that was encapsulated, absorbed onto the surface, or remaining in the filtered solvent. The systematic optimisation of the conditions improved both the yield of the complex and the IE of the AM agents compared to previously reported methods that have been applied to other agents. Using a 1:1 mole ratio of the AM agent to β-CD, the optimised parameters resulted in maximum yields of 87, 84 and 86% (w/w) for thymol, carvacrol and linalool, respectively, with IE's close to 100% (w/w) for each agent.