Adaptation of crops to an increasing range of environmental conditions will be substantial for future plant breeding. EARLY FLOWERING 3 (ELF3) is an important regulator of various physiological and developmental processes and hence may serve to improve plant adaptation. To expand the limited knowledge on barley ELF3 in determining yield formation, we conducted field studies with heterogeneous inbred families (HIFs) derived from selected lines of the wild barley nested association mapping population HEB-25. During two growing seasons, phenotypes of nearly isogenic HIF sister lines, segregating for exotic and cultivated alleles at the ELF3 locus, were compared for ten developmental and yield-related traits. We show that HIF lines, carrying the exotic ELF3 allele, accelerated plant development and were able to increase yield-related traits compared to the cultivated ELF3 allele. Furthermore, the ELF3 coding sequences were used to determine ELF3 proteoforms, where a single amino acid substitution likely leads to an altered protein structure of ELF3, thereby directly affecting phase separation behaviour and nano-compartment formation of ELF3. Possibly, the effect of this substitution is also affecting the disorder-driven phase separation events within the cellular community of ELF3, and, ultimately, regulates a functional complex, thus causing significant trait differences between HIF sister lines.