This study aimed to investigate the influence of phytochemical profile, particularly phenolic compounds, on cotton somatic embryogenesis induction. The research focused on identifying significant differences between recalcitrant and embryogenic cultivars. The analysis demonstrated that embryogenic cultivar Coker 312 exhibited a higher concentration of specific phenolic compounds than non-embryogenic cultivar R405–2000. The superior embryogenic capacity of cultivar Coker 312 is linked to catechin accumulation, which is essential for callus induction. Additionally, other compounds, including catechin, kaempferol, quercetin, E- resveratrol, and p-coumaric acid, are indispensable for embryogenic structure induction in cell suspensions. These phenolic compounds may be utilized as markers for somatic embryogenesis induction of cotton. Conversely, elevated levels of gentisic, salicylic, caffeic, and ferulic acids, accompanied by diminished concentrations of gallic, o-coumaric, and E-cinnamic acids induced by cultivar R405–2000, impede the process of somatic embryogenesis. Additionally, it synthesizes genistein, rutin, E-2, and Z-2 methoxycinnamic acids, which have been demonstrated to have no promoting effect on somatic embryogenesis process. Moreover, incorporation of phenolic compounds identified as markers into the culture medium was unsuccessful in triggering embryogenic structure induction with cultivar R405–2000, indicating that the endogenous synthesis of these phytochemical compounds is the paramount factor. In a nutshell, the impact of the phenolic profile on the embryogenic capacity of cells demonstrates the genotype dependence of somatic embryogenesis in cotton. To overcome this recalcitrance, cells should be capable of synthesizing phenolic markers, potentially through the incorporation of phenolic biosynthesis precursors in the culture medium of callus and cell suspensions.