The former head of a city-funded Main Streets nonprofit faces charges that he embezzled nearly $20,000 in funds intended for community revitalization, authorities announced Tuesday after a 15-month ­investigation.

Carlos Schillaci, 58, worked as the executive director for the Hyde/Jackson Square Main Streets organization in Jamaica Plain for 2½ years before he was suspended in July 2011, when Boston police, city officials, and the nonprofit’s board began investigating financial ­irregularities.