Comprehensive transcriptomic and proteomic analyses were performed to gain further understanding of the molecular mechanisms of floral initiation in Agapanthus praecox ssp. orientalis. Samples of stem apexes were collected at three different time points including the vegetative, induced, and reproductive period. A total of 374 transcript-derived fragments and 72 proteins showed significant differential expression between the samples. The largest proportion of the identified genes and proteins are involved in metabolism, followed by signal transduction, protein fate, cellular transport, and biogenesis of cellular components. A large number of these genes and proteins were upregulated during the induced and reproductive stages. Their expression profiles demonstrate that carbohydrate metabolism provides nutrients foundation for floral initiation in Agapanthus. Furthermore, a transcription factors GAI (GA insensitive protein) that negatively regulates gibberellin signaling, auxin receptor protein TIR1 (Transport inhibitor response 1), a key enzyme of ethylene biosynthesis SAMS (S-adenosylmethionine synthase), and ethylene receptor protein ETR were isolated and identified. Expression patterns of these proteins, in combination with the results of quantitative phytohormone and immunolocalization analyses, indicated that GA, indole-acetic acid (IAA), and ethylene regulate floral morphogenesis and flowering. In conclusion, these data provide novel insight into the early regulatory steps of flowering in Agapanthus.