Like many Quiapo houses, the house has two main entries: a large wooden street door and an iron gate leading to the quay behind. Until the 1930s, the canals were clean and brought to the city provincial cascos laden with grass, sand, and jars of vinegar.
Upstairs there are four long suites of several bedrooms. One of them served as the shop for diamonds and the Nakpil gold pieces which were drafted in the atelier on the ground floor by the river. The public rooms were spacious, for the doctor who loved to throw parties where two orchestras would play. Excluding the kitchen and azotea, the upper story measured 22.45 meters by 15.90 meters.
There are some unforgettable vistas within the house. Unlike the usual doors of the period, the doors separating the dining rooms, antesala and sala slide in sills and can be pushed to the sides. They thus create a vista of a series of doorways leading to a wide exterior window bright with light.
The Nakpil-Bautista house survives to this day. Despite a few alterations, it preserves much of its structure. Unfortunately, the furniture has long been divided among the heirs.