• Yaf9 deletion promotes white-to-opaque switching in MTLa/α heterozygous cells, bypassing MTL repression.
• Yaf9 acts as a repressor of white-to-opaque switching independently of MTL gene regulation.
• Yaf9 deletion in MTLa/a cells leads to a novel elongated opaque morphology (e-Op cells) under 20% CO2.
• The study reveals a conditional role of Yaf9 in cell size control, distinct from filamentous growth.