Inhibition of radial growth and spore germination of Aspergillus niger in media with added chitosan were detected. The highest radial growth inhibition (73%) was determined at 24 h with 3 g · L?1 of chitosan, and the percent inhibition of spore germination was 40% after 13 h of inoculation. Further, the CC50, that is, the concentration at which spore germination is inhibited by 50%, was estimated by probit analysis (3.5 g · L?1). The activation energies, EA were estimated by an Arrhenius model in control and amended chitosan media, obtaining 35.6 and 36.6 kcal · mol?1, respectively. These values were in the same order of magnitude because chitosan as inhibitor was more effective at low temperature (≤ 18 °C). Hence synergism of temperature and chitosan were only observed at 12 and 18 °C. Therefore, the maximal percentage of germinated spores, Smax was also affected by low temperatures in chitosan‐amended media with estimated values lower than 70% at temperatures < 37 °C whereas in control media Smax reached values close to 100%. Scanning electron micrographs showed that chitosan produced spore aggregation and morphological anomalies affecting swelling, germ tube emergence, and polarization.