Abstract Research surveys are important to evaluate fishery resources’ spatial distribution and abundance. Although the underlying sampling is usually conceived with a focus on specific species, efficient designs can also collect data on secondary species. We present a framework to explore and evaluate the adequacy of alternative sampling designs for fishery research surveys aiming to maximize accuracy estimates of the secondary species abundance while maintaining the quality of the abundance estimates of primary species. A geostatistical model-based approach was developed considering the semi-continuous nature of the data and the excess of zero values commonly observed for secondary species. New sampling designs were defined according to optimization weights and evaluated based on the resulting prediction exactness. The framework was applied to the bottom trawl survey conducted along the Portuguese continental coast with European hake, Merluccius merluccius, as the primary species and thornback ray, Raja clavata, as the secondary species. The sampling design URSI provided the best balance between the accuracy for both primary and secondary species. The methodology can be replicated for other bottom trawl research surveys and an extended set of species. We recommend that a decision on which sampling design to adopt in future surveys should consider a cost-efficiency analysis.