Abstract As the industry continues to explore the benefits of continuous and intensified manufacturing, it is important to assure that the cell line development (CLD) workflows in practice today are well suited to generate clones that meet the unique challenges associated with these processes. Most cell lines used in intensified processes are currently developed using traditional fed‐batch CLD workflows followed by adaptation of these cell lines to perfusion processes. This method maybe suboptimal as fed‐batch CLD workflows select clones which produce high volumetric titers irrespective of cell growth rate and specific productivity (qP). Although sufficient for fed‐batch processes, performance of cells derived from this traditional CLD workflow may not be maintained in perfusion processes, where an intricate balance of performance parameters is needed. Until now, a thorough investigation into the effect of the CLD workflow on top clone performance in perfusion processes has not been conducted. Here, we show how the CLD workflow impacts cell performance in both fed‐batch and perfusion processes, emphasizing the advantages of adopting a perfusion‐specific CLD workflow which includes the use of medium specially designed for expansion and production in a perfusion setting, scale‐down models which more accurately simulate perfusion process, and the adoption of perfusion‐specific cell line selection criteria. Together, this results in the development of more efficient cell lines, fit for continuous and intensified processing.