Regulatory compliance of experimental releases into the environment of not yet approved genetically modified plants often requires implementation of measures to reduce the dispersal of reproductive material. To study the impact of nets on pollen flow in an experimental field site in Switzerland, non-GM apple varieties ‘Ladina’ and ’Nicogreen’ were planted inside and outside a netted plot, respectively. Seeds harvested from mature fruits were germinated and the paternal variety of the seedlings was determined using simple sequence repeat (SSR) molecular markers. We demonstrate that pollination frequency from trees inside the netted plot to trees outside over a two-year (2018 and 2019) study of 4500 seedlings is 0.6% (26 seedlings). Moreover, these outcrossing events decreased with increasing distance from the pollen donor. Over the study period, we found on average 0.9%, 0.5%, 0.4% and 0.09% of the seedlings derived from apples of ‘Nicogreen’ trees at 8 m, 15 m, 72 m and 117 m being generated by fertilisations of ‘Ladina’ pollen, respectively. In comparison, 48.3% (2018 season) and 75.1% (2019 season) of examined ‘Ladina’ seedlings in the netted plot originated from ‘Nicogreen’ tree pollen outside the netted plot. The results suggest that insect netting is effective in minimizing egress of apple pollen from an experimental site and that the likelihood of outcrossing is reduced further (<0.1%) when there are no compatible apple trees within a radius of 100 m of the pollen donor. These data are important for biosafety research/regulation to aid understanding of pollen flow in experimental field sites.