The high content of bioactive compounds in the microalga Spirulina platensis has recently attracted attention from food and pharmaceutical industries. However, for its application an effective preservation technique must be developed. In this paper, we investigated the use of a non-conventional rotary dryer (with an inert bed) for drying the microalga Spirulina biomass and the effects of the operational conditions (air temperature, intermittent feeding interval, filling degree of inert particles, and rotation speed) on its bioactive compounds. The results indicated that this non-conventional drying system offers an effective alternative for expanding the use of this biomass in an adequate form. We identified the conditions in which the dried material had maintained satisfactory contents of phenolics (air temperature of 70°C and intermittent feeding interval of 10min), flavonoids (intermittent feeding interval of 17.4min), and phycocyanin compounds (air temperature of 40°C), which were near to those present in fresh microalga.