St Margaret's church was an integral part of Lowestoft in a manner which cannot be fully understood today. At the time that it was built, during the late medieval period, the Roman Catholic ecclesiastical structure throughout the whole of Western Europe was still largely intact and functional. A set of common beliefs was mainly adhered to by the various nations and their leaders, although dissatisfaction with papal authority manifested itself from time to time, as did matters of Biblical interpretation and sacramental practice. John Wyclif and the Lollard movement in late fourteenth- and early fifteenth-century England, for instance, can be seen as foreshadowing the storm that was eventually to break in 1517 when Martin Luther nailed his ninety-five theses to the door of All Saints Church, Wittenberg. But, for the most part, Catholic Europe was united (in a religious sense) by a set of common beliefs and values, which were not always adhered to on a personal or national level but which would have at least elicited lip-service on the part of most people.

Just how much a local parish church mattered to its congregation is hard to assess, but its presence was often sufficiently important for those who could afford it to pay for its construction. Once built, it was as much a statement of civic pride and personal affluence as God's house. But it was there for everyone, in the sense that people were baptised in its font, married at its door (within a porch, or not) and eventually laid to rest in its burial ground. The first two of these services provided were sacraments in their own right and, along with committal to mother earth, were the most fundamental acts for the majority of people. Of the other five recognised sacraments, one (the ordination of priests) did not concern them at all and another (mass) usually involved them directly only once a year – mainly, at Easter. Commitment to the other three – confirmation, penance and extreme unction – was probably desultory in nature and dependent in part on an individual's social and economic standing.