Insect pests affecting standing and stored crops can cause severe damage and reduce yields considerably. Was this also the case in Neolithic Europe? Did early farming populations take a certain amount of harvest loss into account? Did they decide to change crops or rotate them when they became too infested? Did they obtain new crops from neighbouring communities as part of this process? Or did they actively fight against pests? This paper focuses on pulse crop pests, presenting the earliest evidence of fava beans displaying boreholes and of the presence of pea weevil in two different archaeological sites: Can Sadurní (in a phase dated to ca. 4800-4500 cal BC), located in the NE Iberian Peninsula and Zürich-Parkhaus Opéra (in a phase dated to ca. 3160 BC), located in Central Switzerland. Evidence suggests that early farmers were aware of the damages produced by pests and we propose different strategies for their management, including potential evidence for the use of repellent or trap plants in the plots.