Vila Franca Islet was discovered no later than 1537—the year written documents first attest to its existence—as early settlers of São Miguel moved west from their original settlements.[1] In the past the islet accommodated various human activities and uses, including a military fort, a port, vineyards, and a whale watch.[1] Historically the eastern part of the islet was used for butchering dolphins, and is therefore known locally as the Baixa da Cozinha ("kitchen reef").[2][3]

Until 1982 one family privately owned the islet. This family holidayed and maintained vineyards on the islet, producing wine for local consumption.[2] Apparently they were responsible for bringing invasive species to the islet, including Arundo donax which they used as hedges.[2][3]