Most art historians see the panel as the left wing of a dismantled diptych; presumably its opposite wing was a votive portrait. Near-contemporary copies by the Master of 1499 and Jan Gossaert pair it with two very different right-hand images: one is of a donor kneeling in an interior setting; the other is set outdoors, with the donor being presented by St Anthony. Both painters made significant alterations to van Eyck's composition, which may have brought the image more up to date with contemporary styles, but the copies have been described as "spiritually if not aesthetically disastrous to the original concept".
Madonna in the Church was first documented in 1851. Since then its dating and attribution have been widely debated amongst scholars. At first thought an early work by Jan van Eyck, and for a period attributed to his brother Hubert van Eyck, it is now definitively attributed to Jan and believed to be a later work, demonstrating techniques present in work from the mid-1430s and later. The panel was acquired for the Berlin Gemäldegalerie in 1874. It was stolen in 1877 and soon returned, but without its original inscribed frame, which was never recovered. Today Madonna in the Church is widely considered one of van Eyck's finest; Millard Meiss wrote that its "splendor and subtlety of [its depiction] of light is unsurpassed in Western art."
The attribution of the panel reflects the progression and trends of 19th and 20th-century scholarship on Early Netherlandish art. It is now thought to have been completed c. 1438–40, but there are still arguments for dates as early as 1424–29. As with the pages ascribed to Hand G in the Turin-Milan Hours manuscript, the panel was attributed to Jan's brother Hubert van Eyck in the 1875 Gemäldegalerie catalogue, and by a 1911 claim by art historian Georges Hulin de Loo. This is no longer considered credible and Hubert, today, is credited with very few works. By 1912 the painting had been definitively attributed to Jan in the museum catalogue.