Specific devices that combine 96-well plates and high-throughput vials were recently proposed to improve the efficiency of formulation screening. Such devices make it possible to increase the number of formulations tested while reducing the amount of active ingredients needed. The geometry of the product container influences the heat and mass transfer during freeze-drying, impacting product temperature (T_{p}) and therefore affecting the final product quality. Our study aimed to develop a tool to identify the operating conditions resulting in the same Tp when using high-throughput vials inside well plates and serum vials. Heat transfer coefficients between the shelf and the high-throughput vials (KV) were measured using the gravimetric method at chamber pressures ranging from 4 to 65 Pa for a batch of 576 vials located at the center of the well plates. KV distributions were used to predict TP distributions during primary drying of a 5% sucrose solution. Tp values were in average 8 °C higher using high-throughput vials instead of serum vials at chamber pressures lower than 12 Pa. This study provides a graphical solution for the management of process scale-up and scale-down between both types of product containers depending on their respective KV and product resistance to mass transfer.