Magnetospheric substorms drive energetic electron precipitation into the Earth's atmosphere. We use the output from a substorm model to describe electron precipitation forcing of the atmosphere during an active substorm period in April–May 2007. We provide the first estimate of substorm impact on the neutral composition of the polar middle atmosphere. Model simulations show that the enhanced ionization from a series of substorms leads to an estimated ozone loss of 5–50% in the mesospheric column depending on season. This is similar in scale to small to medium solar proton events (SPEs). This effect on polar ozone balance is potentially more important on long time scales (months to years) than the impulsive but sporadic (few SPE/year versus three to four substorms/day) effect of SPEs. Our results suggest that substorms should be considered an important source of energetic particle precipitation into the atmosphere and included in high-top chemistry-climate models.