Since the structure of garden has disappeared by now, the Panipat mosque's location within it is not known. However, the building's enormous size suggests that it, rather than the garden, had dominated the complex. The rectangular prayer chamber, measuring 53.75 by 16.50 metres, is dominated by a large central domed bay flanked on either side by three-bayed triple-aisled side wings. Each bay of the side wings is entered by an arched opening supported on massive piers. Over the mosque's brick construction is a heavy stucco veneer, reminiscent of that covering much Delhi Sultanate architecture. The northwest and southwest corners of the mosque were marked by octagonal towers crowned by domed pavilions, although only one survives. Each of the mosque's bays is surmounted by a dome, those over the westernmost aisle being smaller than those on the east. It comes thus as a foregone conclusion that mosques during Babur, with such instances like the one being described in Panipat in Karnal presently, were only just the humble beginnings, which do stress much on the genius and merit of such a man like Babur as an emperor with such less royal treasury and even less assistance! Indeed, it is also an acknowledged fact that Babur's mosques were taken up in later Mughal times as the exemplary kinds, upon which much of the royal household had assayed to build upon in the religious domain.
Panipat mosque's large central bay's qibla (the direction that should be faced when a Muslim prays during Salah) wall, the one oriented toward Mecca, is stone-faced, but elsewhere the veneer on the mosque's interior is stucco over a brick core. This central bay is the mosque's focal point, visible even from the outside through the wide entrance. Attention is drawn to the mihrab (a niche in the wall of a mosque that indicates the qibla, that is, the direction of the Kaaba in Mecca and hence the direction that Muslims should face when praying; the wall in which a mihrab appears is thus the "qibla wall) by an epigraph - including the Throne Verse from the Quran, and an historical inscription dated 1527-28 - rendered dramatically in black stone against white marble. This very first instance of a mosque during Babur in such primeval times only heightens the emotion of an admirer amidst such meticulousness of 'Mughal-ish' architecture. While the Panipat's mosque's chamber itself is a simple domed structure, recalling the Lodi Bara Gumbad built in Delhi's Lodi Gardens in 1494, the appearance of net pendentives here used only decoratively, evokes a Timurid flavour. Each side wing is divided into two aisles by massive brick piers; the resulting bays are crowned by domes resting on brick pendentives that are covered by a thick stucco veneer, modelled to resemble net squinches, introduced to north India exclusively by the Mughals.
A stone gate stands in the courtyard's north wall amidst the Panipat's mosque of Babur in Karnal. It is carved in the tradition of earlier Lodi gates, for example that at the Lodi-period tomb of Khwaja Khizr dated 1522-24 in nearby Sonepat. Most of the enclosure wall has disappeared in contemporary times, but remains suggest that the entire courtyard was walled and that each side had similar gates.
The Panipat mosque's prayer chamber appears to have been loosely modelled on the type of congregational mosque utilised by the Timurids. It also incorporates features of mosques built by the pre-Lodi sultans in this region. This mosque type, however, was favoured by Babur not because of any earlier Indian associations, but for two rather different reasons. First, it is decidedly different from the single-aisled multi-bayed type, used exclusively by Babur's immediate predecessors, the Afghan Lodis. Notably at Panipat, the site of this mosque, Babur had defeated the Lodis. Second, it is a type that, although somewhat transformed in the process of Indian translation, had been constructed by Timur, for example in his Bibi Khanum mosque in Samarkand. As the Mughal Babur was the only surviving Timurid ruler ruling in India, it must have been especially important for him to preserve at least a vestige of Timurid architectural forms. Thus one notices here precisely that mosques and its architecture during Babur were an intelligent amalgamation of Persian ancientness and the Delhi Sultanate recentness, both nearly witnessed and recognised by a Mughal Babur.
Two other mosques remain that were constructed by leading nobles following Babur's orders. Probably these orders were general ones, not commands to erect specific mosques. One of these mosques is at Sambhal, approximately 140 km east of Delhi. It was constructed in 1526 by Mir Hindu Beg, an important noble in the court of both Babur and Humayun. Built a year before Babur's Kabuli Bagh mosque in Panipat, the Sambhal mosque is the first extant Mughal building in India - also counting as an undisputable mosque construction during Babur and his noblemen's patronage. The complex is entered through a gate on the east that opens to a large walled courtyard. The prayer chamber, like the one of the Panipat mosque, is rectangular with a large square central bay. Its entrance is set into a high pishtaq, recalling those of Sharqi mosques at Jaunpur. The chamber is flanked on either side by three-bayed double-aisled side wings. A single dome surmounts the central bay and a small flatish dome surmounts each bay of the side wings. The mosque's pishtaq and other features resembling fifteenth-century Sharqi structures in nearby Jaunpur, suggest a reliance on local artisans and designers.
Even though the Sambhal mosque was renovated at least twice in the 17th century, enough of its original state remains to demonstrate that the plan and general appearance anticipate Babur's Panipat mosque commenced the following year. The size (40.5 by 12.4 metres), too, anticipates the scale of Babur's imperial mosque, thus making this mosque at Sambhal the largest one constructed in the Delhi region since Timur's sack of that city in 1398. This mosque by Babur is situated high on a hill and dominates the city for a considerable distance. According to Hindu lore that was known to the Mughals, the tenth and last incarnation of Vishnu will appear in Sambhal at the end of this era (yuga).
A second mosque probably built in response to Babur's general orders, not a specific command, stands at Ayodhya, today in Faizabad District, on the banks of the Ghaghara river. Three inscriptions indicate it was constructed by Mir Baqi, a noble, in 1528-29, that is, after the mosques at Sambhal and Panipat. Unlike the other mosques built under Babur's auspices, this one at Ayodhya is a single-aisled three-bayed kind. It is also considerably smaller than the other two. The central bay's pishtaq is much higher than the flanking side bays, but all three bays contain arched entrances. Most of the mosque is stucco-covered, over a rubble or brick core, but carved black stone columns from a pre-twelfth-century temple are embedded into either side of the central entrance porch. The Ayodhya mosque - yet another diversified instance of mosques constructed during Babur, is surmounted by three prominent domes.
This site today however is highly charged. Indeed, it needs to be noted that this mosque being described in Ayodhya is historic and legendary as the Babri Masjid as one knows today for much separate religious conflicting reasons. Many claim the Babri Masjid, situated on a hillock, had replaced a temple which Babur had destroyed. Today this mound popularly is considered the birthplace of the Hindu deity Lord Rama, thus answering to the conflicts of a Hindu-Muslim religious division upon such a mosque during Babur's ancient times in India. An important Mughal chronicler, writing approximately seventy years after the Babri Masjid's construction, acknowledges Ayodhya's sanctity as Rama's dwelling, states nothing about the exact site of Rama's birth. It is thus difficult to disentangle recent popular passion from historical accuracy in association with Ayodhya's mosque by Babur.
All the same, Ayodhya was a site of great importance to Babur's Hindu subjects during the Mughal period. The incorporation of older Hindu architectural members prominently displayed on the mosque's facade, at a period when the reuse of Hindu material was highly unusual, suggests the patron, Mir Baqi, was attempting to make a general statement of Muslim superiority. The Babri Masjid, then, like the others of Babur's time, appears to be located in an area owned a charged significance. Babur's own mosque in Panipat was built on the site of Lodi defeat and Mughal victory, while the other two sites were both associated, however loosely, with ancient Hindu tradition. As such, the mosques during Babur with instances like Babri Masjid do incorporate united endeavours of Islamic-Hindu religious constructions, highly unlike in present Indian times.
Babur's choice of Panipat for a mosque is not difficult to understand. However, the construction of mosques during Babur on sites associated with non-Islamic tradition is less comprehensible, for a ruler who had claimed his right to sovereignty based on his Timurid heritage and Turkish-ness, not on religious grounds. While such rhetoric predominated during his pre-India conquest, once the emperor had established himself permanently in India, Babur had added the establishment of Islam as a mission of his rule. He had referred to Hindus as kafirs, i.e., pagans or infidels and war against his greatest Indian threat, Rana Sangam, was termed jihad or holy war. Shortly after his victory over Rana Sangam, Babur had assumed the title Ghazi, i.e., a warrior dedicated to the cause of Islam and had penned a verse stating his resolve to defeat Hindus and pagans. All such rhetoric followed the long-established practice of Islamic rulers conquering non-Islamic lands. The placement of the Ayodhya and Sambhal mosques by Babur's nobles in generally charged locales was well in keeping with the spirit of Babur's new 'legitimising rhetoric'.
Babur had ruled Hindustan for less than five years before his demise in December, 1530. Although the Mughal emperor had ruled for only a short time, this man was that individual who had introduced Timurid architectural concepts and most importantly, the rationally organised four-part paradise garden. This latter in particular was to become a Mughal trademark, which very much was incorporated within the mosques during Babur as well as, during his generations to come to rule a Mughal India.