When the Franciscans arrived in 1641 looking for a place to set up a clandestine church in Amsterdam, they chose, of all places, the heart of the city's Jewish quarter. The reasoning was practical. The Jodenbuurt had only recently been settled by Sephardic and Ashkenazi refugees who had built their own hidden synagogues - communities that knew how to worship out of sight of Protestant authorities tended to ask fewer questions about their neighbors doing the same. The Franciscans rented a house called Moyses, after the wall tablets of Moses and Aaron that decorated its facade. By 1682 they had bought the neighboring house called Aaron. The two adjacent houses, named for the Old Testament brothers, gave the hidden church behind them its enduring nickname. In 1690 a Dr. Johannes de Vroom, the brother of one of the priests, consolidated four properties into a single block. The expansion of the church had already begun without permission. A new facade went up in 1759. The two houses still stood in front of it. From the street, you could not see a church at all.

The prohibition on Catholic worship in the Netherlands gradually relaxed in the late 18th century and was formally lifted under the Batavian Republic. By the 1830s the Mozes en Aaronkerk could finally announce itself, and between 1837 and 1841 the Franciscans demolished the old hidden structure and replaced it with the building that stands today. The architect was the Flemish-born Tilman-Francois Suys, working in the neoclassical style the era demanded. The twin-towered facade is said to have been modeled on Saint-Sulpice in Paris and Santissima Trinita dei Monti in Rome. The columns are Bentheim sandstone, quarried in Lower Saxony. The plastered brick facade and the painted wood and iron of the towers were a deliberate trick of the eye - the impression of an ancient temple, conjured from cheap modern materials. When Roman Catholic hierarchy was restored to the Netherlands in 1853, the church was raised to parish rank under its original saint's name in 1857. The hidden Sint-Anthoniuskerk had officially become a church.

The church sits diagonally across Jodenbreestraat from the house where Rembrandt lived from 1639 to 1658 - now the Rembrandthuis museum. The painter's own house went up before the Franciscans arrived in the neighborhood; he watched the Catholic church take root next to his Jewish neighbors and Christian friends. He died in 1669, more than a century before the prohibition on Catholic worship would lift, but the buildings he knew - the hidden house churches, the early synagogues, the merchant houses on the Breestraat - remained the world he had painted. The view from the church door across the open square of Waterlooplein toward Rembrandt's gabled brick house is one of the more concentrated patches of Amsterdam's seventeenth century: a Jewish neighborhood, a clandestine Catholic parish, and the studio of the country's most famous painter, all within a one-minute walk.

On 26 April 1866, Franz Liszt visited Amsterdam and was treated to a performance of his own Graner Mass by the church's orchestra and chorus under the Dutch conductor Herman van Bree. A plaque with his profile commemorates the visit. The Adema-Philbert organ that may have played for him - built between 1869 and 1871 by the Adema brothers of Leeuwarden, with some pipes from the famous French builder Aristide Cavaille-Coll - was the first organ in the Netherlands to use the Barker lever, a French innovation that allowed for faster, louder playing. By the late 19th century, however, the parish was emptying as Catholics moved to other parts of Amsterdam. The Jewish neighborhood around it survived until the Nazi occupation; the church served as a landmark inside the Nazi-imposed ghetto during the war. The parish was suppressed in 1969. The church sat largely unused. In 2014, after 34 years without a regular liturgy, it was reconsecrated and entrusted to the Community of Sant'Egidio, a lay Catholic movement focused on charitable work, who now run weekly Sunday Mass and weekday prayer services.

There is one quiet thing on the church wall that visitors often miss. On 8 December 1992 - the tenth anniversary of the December Murders in Suriname - a plaque was placed on the side wall of the Mozes en Aaronkerk in memory of the fifteen victims arrested, tortured, and killed without trial by soldiers loyal to the dictator Desi Bouterse on 8 December 1982. Suriname was a Dutch colony until 1975, and a large Surinamese community lives in Amsterdam; the plaque on a Catholic church in a former Jewish neighborhood remembers fifteen Surinamese men whose names should be remembered everywhere. The building has stood for nearly two centuries on a corner that has been, in turn, hidden and revealed, Catholic and Jewish, full and empty. It keeps the count for everyone.