Rhizobium leguminosarum bv trifolii strains TA1 and CC275e have been widely used as effective nitrogen fixing strains for white clover in New Zealand, but rhizobia survival on seeds is usually poor due to different stress conditions. The aim of this study was to select one of those commercial strains grown in a solid carrier (core) and study the influence of the core:polymer ratio in a microencapsulation process by spray drying using guar gum as coating material. First, strains TA1 and CC275e grown on peat and diatomaceous earth were exposed to temperature and desiccation stress. Both strains were stable at 40 °C and completely died after five minutes at 80 °C, while CC275e was more stable than TA1 at 60 °C. TA1 and CC275e slightly decreased viability after six hours drying with either carriers, with no differences between strains. A central composite design was used to develop the microencapsulation process. Independent variables were: inlet temperature (130 °C) and feed flow rate (5 mL/min). Microparticles presented rhizobia loading in 10 CFU/g and mean particle size between 10 and 30 μm. Optimized process reached 50% yield and 10 CFU/g loading. Rhizobia viability dropped two logarithmic units during the microencapsulation/drying process, possibly due to the negative effects of dehydration and high outlet temperature (≈70 °C), suggesting the need to continue optimizing the process by improving the thermal profile in the drying chamber.