The advent of ‘conservation agriculture’ (CA) farming using zero- or no-tillage practices and an accompanying change in crop rotations in the last 10–15 years has potentially led to less disturbance of mouse burrows and increased cover and food supply. Given the irregular outbreaks of mice in grain cropping regions in Australia and the damage they cause, it is important to understand when and where mouse populations increase so that management strategies can be improved. We utilised a 20-year long-term mouse population data set collected prior to the introduction of CA farming practices and a more recent 8-year data set after CA to compare changes in mouse population abundance in a typical dryland grain cropping system in north-western Victoria, Australia. Mouse trapping data were used to compare abundance in crop and margin habitats during crop growth and non-crop (fallow) periods before (‘conventional’) and after introduction of CA. Mice are now resident year-round within crops and stubble and appear to only spill over into margin habitats. Previously developed recommendations for mouse management that include their control while in margin habitats may no longer be valid.