Vaishnavism in the Agamas have contributed towards a fuller and more comprehensive development of the philosophy of Vaishnavism. In the post-Vedic period, a fuller development of the important tenets of Vaishnavism can be found in the Agamas. The Agamas are a body of religious treatises devoted primarily to the modes of worship of God. The term Agama generally means sacred texts and refers in particular to the revealed scripture (nigama). The Agama is also known as tantra or the system that elaborates the knowledge acquired from the Vedas. It is also designated as samhita or the composition.

The dates of the Agamas are disputed among the modern scholars varying from 3000 B.C. to A.D. 800. But according to tradition the main source of the Vaishnava doctrines contained in the Agamas is the Vedas. The Mahabharata in which we have the earliest and clear presentation of the essential teachings of the Pancharatra Agamas states that Lord Narayana is the promulgator of the Pancharatra system. The Vedanta-sutra also makes a reference to the Pancharatra system. Therefore, generally, the Agamas are placed in a period which is later than the Vedas and earlier than the Mahabharata.

There are many different types of Agamas. The ones that are usually considered important are the Vaishnava, Saiva and Sakta Agamas. The Vaishnava Agamas uphold the exclusive worship of Lord Vishnu as the Supreme Deity. Saiva Agamas emphasise the worship of Lord Shiva as the Supreme Deity. The Sakta Agamas regard Sakti or a female energy known by the names of Goddess Devi, Durga, Kali etc., as the Supreme Deity. The Vaishnava Agamas went on to constitute the main source for the later development of the Vaishnavism.

In the Vaishnava Agamas, the concept of Lord Vishnu as the Supreme Deity, as found in the Rig Veda, was developed into a cult. The Vaishnava Agamas emphasize the exclusive worship of Lord Vishnu as a means to salvation. Realizing the need of offering worship to one deity in a concrete form these Agamas have evolved the concept of worshipping it in an image form (area). As a follow up of this form of worship, the consecration of icons, the construction of temples for this purpose and the observance of certain prescribed daily rituals and other festivals in the temples have all been formulated in the Agamas. All these have influenced the development of Vaishnavism.

There are two main categories under which the Vaishnava Agamas fall. These are the Vaikhanasa and the Pancharatra. The former which is older in origin is based on the Vaikhanasakalpa Sutras compiled by the Vedic Sage Vikhanas. The Vaikhanasa claims to have taken its teachings directly from the Vedas. The Vaikhanasa system was expounded by four sages, Marichi, Bhrigu, Atri and Kasyapa who are claimed to be the disciples of Vikhanas. Based on the hymns of the Rig Veda that pertain to the worship of Lord Vishnu, it advocates that Brahmins should perform the archana of Vishnu daily. Vishnu in this system is identified with Narayana, the very Brahman, on the authority of the Taittiriya Upanishad.

The Pancaratra Agamas also have a Vedic origin. They are based mainly on the Ekayana shakha of the Sukla Yajurveda, as a result of which they are said to be of Vedic origin. The term Pancaratra has been interpreted in different ways, and of these, one of the most plausible is the one provided by Vedanta Desika. It is said to teach the fivefold daily religious duty of a Vaishnava, which are abhigamana, upadana, ijya, svadhyaya and yoga. As Ahirbudhnya Samhita explains, the name is also derived from the concept of the fivefold manifestation of the Supreme Being as para, vyiiha, vibhava, area and antaryami. The names which are generally used for Vishnu in these Agamas are Bhagavan and Vasudeva. These names, including that of Narayana are identical. The Ahirbudhnya Samhita has offered a detailed etymological interpretation for these terms. When these terms are taken into consideration, it gets evident that all the names represent the Supreme Being, the very Brahman of the Upanishads.

Some ancient as well as modern scholars have taken the view that Pancaratra is non-Vedic in origin and hence not authoritative. The validity of Pancaratra system has been vindicated by Yamuna in his Agamapramanya, by Ramanuja in his commentary on the relevant Vedanta-sutras and in a more emphatic way by Vedanta Desika in the Pancharatraraksa. The Mahabharata extolls it as authoritative because it is taught by Lord Narayana. The Pancharatra Sarhhitas claim their origin from the Vedas. It is, therefore, definitely pro-Vedic. Sarhkara in his commentary on the disputed Vedanta-sutra regarding the validity of Pancharatra questions only some of its philosophic theories which apparently appear to contradict Vedic teachings such as the origin of the jiva, but he has not openly disputed the essential teachings of Pancharatra theology. In fact, Sarhkara holds in high esteem the Bhagavatas, the four Vyuhas, the concept of Vasudeva as Supreme Deity and the fivefold religious practice of Bhagavatas.

The treatises of the Pancharatra Sarhhitas are many in number. The Sarhhitas themselves enumerate them and the number varies from 108 to 154. They have been written at different periods. A few are most ancient, while many others are of later origin. The most ancient and authoritative Vaishnava Agamas are Sattvata, Pauskara and Jayakhya claiming their source to the divine teachings (divya). Based on these, we have Isvara, Paramesvara and Padma Sarhhitas which have been contributed by the sages (muni-bhasita). Two other Agamas from which material has been drawn extensively by the Vaishnava acaryas for expounding the doctrines of the avatara, Goddess Sri and prapatti are Ahirbhudhnya Samhita and Laksmi tantra. The other important topics which have been adopted by Vaishnavism from the Pancaratra texts are: the six principal attributes of God (sadguna), the mode of worship of God in the form of icon at temples as well as homes, the fivefold daily religious observances, the theory of nitya-vibhuti and paramapada (divine abode) and the concept of Bhagavata.

In general, the theological aspect of Vaishnavism has been greatly influenced by the Pancharatra system. On the philosophic side, the influence of the Agamas has not been so great. The philosophical theories relating to the doctrines of Isvara, jiva, prakrti, their organic relationship, the means (upaya) and goal (moksa) are all taken direct from the Upanishadic teachings.