Emerging adulthood is an important period in the development of one's identity and autonomy. The ways in which identity and autonomy are viewed by emerging adults and how they impact quality of life (QoL) in individuals with early-onset neuromuscular conditions is not yet known. This study focused on understanding and exploring relationships between self-perceptions of emerging adulthood, autonomy, and QoL. Five previously validated measures were incorporated into an online survey and distributed to young adults with early-onset neuromuscular conditions and unaffected controls. Topics explored included individuals' views regarding their overall QoL, disease-specific QoL, components of emerging adulthood, and autonomy. We found that a sense of higher disease impact was associated with a lower Overall General QoL. Additionally, perceptions of key autonomy factors "negativity" and "instability" were uniquely associated with Overall General QoL in the case group as compared to controls, whereas "attitudinal autonomy" (attaining the ability to plan and follow through with goals) was important to this age group regardless of health status. The specific factors of emerging adulthood and autonomy that were significantly correlated with Overall General QoL can be used for developing targeted counseling and interventions to improve QoL for individuals and their families.