The Bakoshi-Kundila Au deposit is located in the Nigerian Shield in West Africa. In this deposit, Au-bearing pyrite contains inclusions of Au-rich hydrothermal quartz. Whether or not this co-precipitation relationship of quartz and pyrite is cogenetic and related to the gold fluid remains untested. The deposit's genetic affiliation is controversial. This study reports the results of textural and in situ chemical compositions of hydrothermal quartz, and sheds light on fluid composition, element substitutions into quartz structure, and inferred the deposit genetic type. We grouped the quartz into four generations: Qz1 and Qz2 (vein-type) and Qz3 and Qz4 (wallrock-type). The Qz2 is deformed, overprinted by late-stage fluid activity. The Qz1 is rich in Ga and Sr but poor in Al and Fe than Qz3 and Qz4: average Ga in ppm (Qz1 – 0.62, Qz3 – 0.08, Qz4 – 0.15), Sr (Qz1– 26.7, Qz3 – 4.59, Qz4 – 5.78), Al (Qz1– 16.7, Qz3 – 82.8, Qz4 – 136), Fe (Qz1– 131, Qz3 – 144, Qz4 – 133). However, the contents of low melting point chalcophile elements (LMCE) are higher and overlapped between Qz1 and Qz3 than those from Qz4: average Au in ppm (Qz1– 33.9, Qz3 – 38.2, Qz4 – 7.83), Cu (Qz1 – 13.1, Qz3 – 14.8, Qz4 – 5.95), Bi (Qz1 – 3.48, Qz3 – 0.25, Qz4 – 0.51). The LMCE in Qz1 displayed covariant relationships with Au (but poorly defined in Qz3 and Qz4), suggesting the likely presence of Au-Ag-(±Te)-bearing phases like petzite and argentum. Aluminum is the main trivalent element substituting Si4+ in Q3 and Qz4, whereas Fe3+ in Qz1. The charge-balanced cations are Li+, Na+, and K+ in Qz3 and Qz4, whereas Sr2+ in Qz1. The Al and Ti contents (in ppm) are higher and more variable in Qz3 (Al: 5.97–374, avg 82.8; Ti: 2.69–12.5, avg 6.60) and Qz4 (Al: 8.13–792, avg 136; Ti: 7.64–72.0, avg 20.2), which may imply fluctuation in fluid pH. These element concentrations are lower and less variable in Qz1 (Al: 5.25–47.8, avg 16.7; Ti: 3.41–18.0, avg 5.43), suggesting a less acidic and probably stable pH condition during its precipitation. The Qz1 has a lower average content (in ppm) of compatible elements (K – 15.7, Fe – 13.1, Ti – 5.43) than Qz3 (K – 25.9, Fe – 144, Ti – 6.60) and Qz4 (K – 63.0 Fe – 133, Ti – 20.2), implying that Qz3 and Qz4 precipitated at a higher temperature than Qz1. However, the contents of the incompatible elements (e.g., P, Ge, Rb, and Li) are not enriched in the supposed lately-formed Qz1 over Qz3 and Qz4, which is inconsistent. The inconsistency is also true between the wallrock type, with lower contents in low-temperature Qz3 than in high-temperature Qz4. Thus, temperature is considered not a major controlling factor during the formation of Bakoshi-Kundila quartz; instead, the pH condition and fluid-rock reaction are favored. The Bakoshi-Kundila quartz has Al-Ti contents akin to quartz from orogenic Au deposits.