The quality of field crop establishment is an indicator of the productivity and yield quality of a given crop. Several biotic and abiotic factors, as well as cropping practices, affect the quality of field crop establishment. More specifically to soybean, recent studies quantified pre-emergence seedling losses and identified the associated causes of non-emergence. However, little is known about post-emergence seedling damage, mainly due to vertebrate pests, which represent an important problem for growers. A 2-year field observation was conducted to quantify near- and post-emergence seedling damage due to vertebrate pests. The common wood pigeon (Columba palumbus) and the European hare (Lepus europaeus) were associated with this kind of damage. The characteristic damage due to the common wood pigeon consisted of either partially-damaged cotyledons during emergence or completely uprooted seedlings at emergence. In contrast, damage due to the European hare consisted of chewed seedling or seedling parts. There was significant effect of year (p < 0.001) on the final rates of post-emergence seedling damage due to the wood pigeon but not on those due to the European hare. The final rates of post-emergence damage due to the wood pigeon were higher (32% for 2018 and 22% for 2020) compared with those owing to the European hare (18% for 2018 and 17% for 2020). The severity of damage due to vertebrate pests was related to the type of seedling damage that, in turn, affected the capacity of soybean to compensate for post-emergence seedling damage.