As a substitute of traditional fossil fuels, biomass is widely used to generate electricity and heat. The temperature of stored biomass needs to be monitored continuously to prevent the biomass from self-ignition. This paper proposes a non-intrusive method for the temperature measurement of stored biomass based on acoustic sensing techniques. A characteristic factor is introduced to obtain the sound speed in free space from the measured time of flight of acoustic waves in stored biomass. After analysing the relationship between the defined characteristic factor and air temperature, an updating procedure on the characteristic factor is proposed to reduce the influence of air temperature. By measuring the sound speed in free space, air temperature is determined which is the same as biomass temperature. The proposed methodology is examined using a single path acoustic system which consists of a source and two sensors. A linear chirp signal with a duration of 0.1 s and frequencies of 200-500 Hz is generated and transmitted through stored biomass pellets. The time of flight of sound waves between the two acoustic sensors is measured through correlation signal processing. The relative error of measurement results using the proposed method is no more than 4.5% over the temperature range from 22 degrees C to 48.9 degrees C. Factors that affect the temperature measurement are investigated and quantified. The experimental results indicate that the proposed technique is effective for the temperature measurement of stored biomass with a maximum error of 1.5 degrees C under all test conditions.