The Esnoga's design is credited to Elias Bouman, with the city architect Daniel Stalpaert also named in connection with the plan, and the building the two produced still repays close architectural attention beyond the candlelight the congregation is best known for keeping. The main sanctuary runs roughly thirty six by nineteen meters beneath a soaring wooden barrel vault, carried on twelve tall stone columns, one for each of the twelve tribes of Israel, with a women's gallery running along three sides above the congregation below.
Underfoot the building keeps a custom now almost extinct among working synagogues. A thin layer of fine sand covers the sanctuary floor, laid down originally to absorb moisture tracked in on worshippers' shoes and to soften the sound of footsteps on stone, and the Esnoga is one of only five synagogues left anywhere in the world still maintaining a sand floor rather than having replaced it with tile or wood at some point in three and a half centuries of continuous use.
The wider synagogue complex, arranged around a small courtyard, houses more than the main sanctuary alone. Smaller buildings hold a winter synagogue used in the colder months, offices, the rabbinate, and Ets Haim, one of the oldest working Jewish libraries anywhere in the world, its collection assembled by the same Sephardic community that built the sanctuary above the sand. Taken together, the columns, the sand and the library describe a congregation that built not one landmark building but a small, largely self sufficient institution, and kept it running as one for three hundred and fifty years.