The COVID-19 crisis has stressed the importance of, and need for, a stable and functional food system, able to provide consumers with a continuous supply of quality food at affordable prices. The pandemic has also highlighted the role of agricultural producers in the food supply chain, with small farmers being the most vulnerable category. This global crisis has actually deepened the problems faced by farmers, especially those on the verge of sustainability. The purpose of this analysis was to provide an overview of the disrupted links in agriculture, as a result of the initial COVID-19 crisis. A survey was carried out with 91 farmers in North Macedonia. Moreover, in-depth interviews were conducted with selected traders and processors. In general, farmers assessed that the crisis negatively affected their economic operations. The critical parts of the supply chain derive from the disrupted link between farmers and traders/processors, lack of field technical support resulting from the mobility restrictions, uncertainty in cooperation, lower production quantities, and varying quality of the agricultural products. Availability and cost of seasonal workforce was also pronounced as an issue. The dominant family farms small-scale structure and lack of aggregation in the sector challenged the resilience and effective response to the crisis. From buyers’ and processors’ perspective, the crisis effect was marked through the disrupted communication with farmers, low awareness of the need for change, and drastic decline in the HORECA channel sales. The agricultural and rural policy is designed to address measures adjusted to the needs of the key actors in the sector. The priority set of measures should support the food supply chain, enhancing farmers’ networking and aggregation, and on-farm and off-farm diversification, along with improved communication, information systems and digitalisation. Improving productivity and competitiveness remains an effective strategy for sustainable operations, greater resilience and risk adaptation in crises such as the pandemic.