He was born into the notable Hydriot family of Miaoulis, which had played a prominent role in the Greek War of Independence.
After independence, Emmanouil Miaoulis joined the newly established Royal Navy.
In 1853, after a distinguished service, he was appointed to teach the first classes in theoretical navigation in the recently founded Hellenic Naval Academy, aboard the corvette Loudovikos.
He then was assigned as captain of the steam schooner Panope, and was sent to Britain to sail it home.
Exonerated by the subsequent court martial, in 1857 he was sent back to England to receive another newly built steam schooner, the Afroessa.