Coffee seed development is accompanied by severe modifications in water soluble proteins, several of these being associated to a specific developmental stage. For this reason, a proteomic approach has been used to describe spatial-temporal proteome modifications in zygotic embryos at different stages of seed development. Embryos from Coffea arabica seeds were harvested in two different developmental stages: stage 1 at 210 days after anthesis and stage 2 at 255 days. Total proteins were extracted and submitted to 2-DE. From these gels, several spots were identified by mass spectrometry including kinases, MYB transcription factor and enzymes involved in metabolic pathways. All proteins identified seem to affect coffee development in different ways, being directly involved in plant growth or used as an intermediate in some metabolic pathway that, indirectly, will influence coffee development. This is the first work using two-dimensional electrophoresis followed by mass spectrometry analyses that evaluates the expression of proteins during coffee zygotic embryos development. Data here reported supply some light over coffee development and could be used in a near future to improve coffee plants' growth and development by molecular strategies.