Religious war
Some commentators have concluded that only 123 wars (7%) out of these 1763 wars were fundamentally originated by religious motivations. Andrew Holt (2018) traced the origin of the "only 123 religious wars" claim back to the 2008 book The Irrational Atheist of far-right activist Vox Day, which he notes is slightly adjusted compared to the 121 that is indeed found in the Encyclopedia of Wars itself.
The Encyclopedia of War, edited by Gordon Martel, using the criteria that the armed conflict must involve some overt religious action, concludes that 6% of the wars listed in their encyclopedia can be labelled religious wars.

Holy war concepts in religious traditions: While early empires could be described as henotheistic, i.e. dominated by a single god of the ruling elite (as Marduk in the Babylonian empire, Assur in the Assyrian empire, etc.), or more directly by deifying the ruler in an imperial cult, the concept of "holy war" enters a new phase with the development of monotheism.

Ancient warfare and polytheism: During classical antiquity, the Greco-Roman world had a pantheon with particular attributes and interest areas. Ares personified war. While he received occasional sacrifice from armies going to war, there was only a very limited "cult of Ares". In Sparta, however, each company of youths sacrificed to Enyalios before engaging in ritual fighting at the Phoebaeum.
Hans M. Barstad (2008) claimed that this ancient Greek attitude to war and religion differed from that of ancient Israel and Judah: "Quite unlike what we find with the Greeks, holy war permeated ancient Israelite society." Moreover, ever since the pioneering study of Manfred Weippert, "»Heiliger Krieg« in Israel und Assyrien" (1972), scholars have been comparing the holy war concept in the (monotheistic) Hebrew Bible with other (polytheistic) ancient Near Eastern war traditions, and found "many [striking] similarities in phraseology and ideology".

Christianity: According to historian Edward Peters, before the 11th century, Christians had not developed a concept of holy war (bellum sacrum), whereby fighting itself might be considered a penitential and spiritually meritorious act. During the ninth and tenth centuries, multiple invasions occurred which led some regions to make their own armies to defend themselves and this slowly lead to the emergence of the Crusades, the concept of "holy war", and terminology such as "enemies of God" in the 11th century. In early Christianity, St. Augustine's concept of just war (bellum iustum) was widely accepted, but warfare was not regarded as a virtuous activity and expressions of concern for the salvation of those who killed enemies in battle, regardless of the cause for which they fought, was common.
During the era of the Crusades, some of the Crusaders who fought in the name of God were recognized as the Milites Christi, the soldiers or the knights of Christ.
The Crusades were a series of military campaigns against the Muslim Conquests that were waged from the end of the 11th century through the 13th century. Originally, the goal of the Crusaders was the recapture of Jerusalem and the Holy Land from the Muslims, and the provision of support to the besieged Christian Byzantine Empire which was waging a war against Muslim Seljuq expansion into Asia Minor and Europe proper. Later, Crusades were launched against other targets, either for religious reasons, such as the Albigensian Crusade, the Northern Crusades, or because of political conflicts, such as the Aragonese Crusade. In 1095, at the Council of Clermont, Pope Urban II raised the level of the war from a bellum iustum (a "just war"), to a bellum sacrum (a "holy war").

Hinduism: This does not refer to religious conflict. Dharma-yuddha in Hindu texts, refers to the protocol to be followed by both parties at war. It sets the rules for both sides to conduct the war fairly (jus in bello). It is important in Vedic and epic literature such as the Mahabharata and the Ramayana. The word Dharma may be interpreted variously as righteousness or responsibility or duty based on the context.  
Neither the Mahabharata nor the Ramayana were religious conflicts. The Mahabharata was fought over the inheritance of the kingdom of Hastinapura. Ramayana was fought over the abduction of Rama's wife Sita by Ravana. The two epics are of great importance in Hindu tradition.
However, according to Torkel Berkke, the Mahabharata does not provide a clear discussion on who has the authority to initiate a war (jus ad bellum), nor on what makes a war just (bellum justum).

Islam: The Muslim conquests were a military expansion on an unprecedented scale, beginning in the lifetime of Muhammad and spanning the centuries, down to the Ottoman wars in Europe.  Until the 13th century, the Muslim conquests were those of a more or less coherent empire, the Caliphate, but after the Mongol invasions, expansion continued on all fronts (other than Iberia which was lost in the Reconquista) for another half millennium until the final collapse of the Mughal Empire in the east and the Ottoman Empire in the west with the onset of the modern period.
There were also a number of periods of infighting among Muslims; these are known by the term Fitna and mostly concern the early period of Islam, from the 7th to 11th centuries, i.e. before the collapse of the Caliphate and the emergence of the various later Islamic empires.

While technically, the millennium of Muslim conquests could be classified as "religious war", the applicability of the term has been questioned.
The reason is that the very notion of a "religious war" as opposed to a "secular war" is the result of the Western concept of the separation of Church and State. No such division has ever existed in the Islamic world, and consequently, there cannot be a real division between wars that are "religious" from such that are "non-religious". Islam does not have any normative tradition of pacifism, and warfare has been integral part of Islamic history both for the defense and the spread of the faith since the time of Muhammad. This was formalised in the juristic definition of war in Islam, which continues to hold normative power in contemporary Islam, inextricably linking political and religious justification of war. This normative concept is known as Jihad, an Arabic word with the meaning "to strive; to struggle" (viz. "in the way of God"), which includes the aspect of struggle "by the sword".
The first forms of military jihad occurred after the migration (hijra) of Muhammad and his small group of followers to Medina from Mecca and the conversion of several inhabitants of the city to Islam. The first revelation concerning the struggle against the Meccans was Quran 22:39-40:

Permission ˹to fight back˺ is ˹hereby˺ granted to those being fought, for they have been wronged. And Allah is truly Most Capable of helping them ˹prevail˺. ˹They are˺ those who have been expelled from their homes for no reason other than proclaiming: "Our Lord is Allah." Had Allah not repelled ˹the aggression of˺ some people by means of others, destruction would have surely claimed monasteries, churches, synagogues, and mosques in which Allah's Name is often mentioned. Allah will certainly help those who stand up for Him. Allah is truly All-Powerful, Almighty.
This happened many times throughout history, beginning with Muhammad's battles against the polytheist Arabs including the Battle of Badr (624), and battles in Uhud (625), Khandaq (627), Mecca (630) and Hunayn (630).

Judaism: Reuven Firestone (2012) stated "that holy war is a common theme in the Hebrew Bible. Divinely legitimized through the authority of biblical scripture and its interpretation, holy war became a historical reality for the Jews of antiquity. Among at least some of the Jewish groups of the late Second Temple period until the middle of the second century, C.E., holy war was an operative institution. That is, Jews engaged in what is defined here as holy war." He mentioned the Maccabean Revolt (167–160 BCE), the First Jewish–Roman War (66–73 CE) and the Bar Kokhba revolt (132–136 CE) as three examples of a "holy war" or "Commanded War" (Hebrew: מלחמת מצווה Milkhemet Mitzvah) in the eyes of Rabbinic Judaism at the time. He asserted that this concept may have re-emerged in modern times within some factions of the Zionist movement, particularly Revisionist Zionism.

In 2016, however, Firestone made a distinction between what he regarded as the Hebrew Bible's concept and the 'Western' concept of holy war:"Holy war" is a Western concept referring to war that is fought for religion, against adherents of other religions, often in order to promote religion through conversion, and with no specific geographic limitation.