The current study sought to investigate the physiochemical conditions and fluid evolution within the Yolindi Cu-Fe skarn mineralization located in the Biga Peninsula, NW Turkey. This was accomplished through a comprehensive investigation of geological and mineralogical data, along with isotopic analyses of sulfur (δ34S), carbon (δ13C), and oxygen (δ18O) of sulfide and calcite minerals, respectively, as well as fluid inclusion data pertaining to various minerals (e.g., andradite, quartz, and calcite). The Yolindi area features a complex geological framework, including the Paleozoic Kalabak Group (which includes the Torasan, Yolindi, and Sazak formations) and the Triassic Karakaya Complex. These formations were subsequently intruded via Early Miocene Şaroluk granitoids and Hallaçlar volcanics. Skarn formation is zoned into endoskarn and exoskarn types (being categorized into proximal, intermediate, and distal zones), with distinct mineral assemblages indicating concentric and contact metamorphic alteration patterns around the western part of Şaroluk granitoid intrusion in contact with the Torasan formation. The ore mineralogy and paragenesis suggest three distinct stages of evolution: an initial phase of prograde metasomatism characterized by the formation of magnetite and pyrite alongside anhydrous calc-silicate minerals; a subsequent phase of retrograde alteration marked by the formation of epidote, actinolite, and scapolite, accompanied by the occurrence of chalcopyrite and specular hematite; and finally, a post-metasomatic stage involving oxidation processes that led to the development of secondary mineral assemblages containing cerussite, covellite, and malachite. Sulfur isotopes (δ34S) of sulfides from endoskarn (from +0.27 to +0.57‰VCDT) to intermediate exoskarn (from −9.44 to −5.46‰VCDT) zones indicate a diverse sulfur source, including magmatic, sedimentary, and possibly organic matter. δ34S values in hydrothermal fluids suggest a magmatic–hydrothermal origin, with endoskarn and proximal zone fluids showing a slight negative signature and intermediate zone fluids indicating a strong influence from organic-rich or metamorphic sulfur reservoirs. Carbon and oxygen isotopic compositions (δ13C and δ18O) of calcite revealed a progression from marine carbonate signatures in marble samples (from +1.89 to +2.23‰VPDB; from +21.61 to +21.73‰VSMOW) to depleted values in prograde (from −6.0 to +0.09‰VPDB; from +6.22 to +18.14‰VSMOW) and retrograde skarns (from −3.8 to −2.25‰VPDB; from +0.94 to +3.62‰VSMOW), reflecting interactions with high-temperature magmatic fluids and meteoric water mixing. The fluid inclusions in prograde minerals generated under the conditions of fluid boiling exhibited high temperatures, reaching up to 412 °C, and salinities up to 26 wt.% NaCl equivalent. Conversely, the fluid inclusions in retrograde minerals, which were generated due to fluid mixing, exhibited lower temperatures (with an average of 318 °C) and salinities with an average of 4.9 wt.% NaCl equivalent. This indicated that the cooler and more diluted fluids mix with meteoric waters and interact with organic materials in the host rocks. This suggests a multifaceted origin involving various sources and processes. Therefore, this study concluded that the skarn mineralization in the Yolindi area resulted from complex interactions between magmatic, metamorphic, and meteoric fluids, reflecting a dynamic ore-forming environment with implications for the regional metallogeny of Cu-Fe skarn deposits.