This data release presents high-spatial resolution geochemical analyses collected from Mesoproterozoic apatite crystals in igneous rocks from the St. Francois Mountains terrane and coeval ore rocks from the Pea Ridge iron oxide-apatite-rare earth element (IOA-REE) and Boss iron oxide-copper-gold (IOCG) deposits. These deposits are located in the southeast Missouri iron metallogenic province. These data support a journal article entitled, “Apatite trace element geochemistry and cathodoluminescent textures—A comparison between regional magmatism and the Pea Ridge IOA-REE and Boss IOCG deposits, southeastern Missouri iron metallogenic province, USA” by Celestine N. Mercer, Kathryn E. Watts, and Juliane Gross, that is published in Ore Geology Reviews. The goal of these data is to use apatite geochemical data to elucidate the petrogenetic histories of the samples and help evaluate ore deposit models. Our sample suite comprises 25 samples, encompassing 8 regional rhyolite suite rocks, including rhyolite host rocks at Pea Ridge and Boss; 6 regional mafic- to intermediate-composition suite rocks, including one intermediate-composition host rock at Boss; 10 ore samples from the Pea Ridge deposit (amphibole-quartz zone, magnetite zone, hematite zone, and REE-bearing hard breccia pipe), and 1 ore sample from the Boss deposit (magnetite-rich ore zone). Prior to quantitative analysis, apatite was identified by petrographic microscope in thick sections and imaged by backscattered electron (BSE) microscopy to distinguish complex textural domains. Apatite crystals contain primary domains as well as secondary and tertiary altered domains. These data were collected at the U.S. Geological Survey (USGS) Denver Microbeam Laboratory using a FEI Quanta 450 field emission gun scanning electron microscope (SEM) equipped with an energy dispersive spectroscopy (EDS) detector operating at 15-20 kilovolts (kV) and a beam current of 0.1-0.5 nanoamperes (nA). Major and minor element analyses in apatite were analyzed at the USGS Denver Microbeam Laboratory using a JEOL 8900 electron microprobe (EMP). We report 283 spot analyses that were completed using a 15 kV accelerating potential, 20 nA beam current, and the largest spot size possible (about 3-10 micrometers [µm]) to analyze a particular apatite domain while minimizing elemental migration. Natural and synthetic minerals and glasses were used as standards for all EMP analyses. Average detection limits are typically about 200-300 parts per million (ppm) for P, Si, Na, and Cl; about 100 ppm for Ca, S; and about 900 for F. This analytical setup is adequate for routine analysis of Ca, P, Si, Na, and S in apatite, but provides F and Cl analyses with relatively larger uncertainties. Given these operating conditions, the generally F-rich, Cl-poor character of the apatite, the random crystallographic orientations of the grains analyzed, and the total beam exposure of 120 seconds (for F, Cl, Ca, and P), we expect there was an increase in F X-ray counts of up to about 30-40 percent and a decrease in Cl X-ray counts of up to about 20-30 percent (Goldoff and others, 2012). Our analytical accuracy for measurements of the F-rich Wilberforce apatite standard is within ≤3 percent for Ca, P, and Na, but high by about 33 percent for F, suggesting F (and presumably Cl) is inaccurate. Nonetheless, we report measured values of F and Cl data because even with these large uncertainties they clearly demonstrate the basic compositional variety between samples. Trace element concentrations in apatite were measured by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) using a Photon Machines Analyte G2 LA system (193 nanometer [nm], 4 nanosecond [ns] excimer) attached to a PerkinElmer DRC-e ICP-MS, housed at the USGS Denver Laser Ablation ICP-MS Laboratory. We report 37 minor and trace elements from 231 apatite spot analyses. Spot ablation was carried out using a 15 to 25 µm spot size at 10 joules per square centimeter (J/cm2) and using 12-14 hertz (Hz) with a 30-second(s) baseline and 40 to 50 seconds of ablation. Ablated materials were transported via a He carrier gas to a modified glass mixing bulb where the He plus the sample aerosol were mixed coaxially with Ar prior to the ICP torch. Concentration and detection limit calculations were conducted using the protocol of Longerich and others, (1996). Concentrations of Ca from EMP analyses were used as the internal standard. The USGS Ca-phosphate material MAPS-4 was used as the primary reference material for all analyses and NIST610 was used as the secondary reference material in all runs. The preferred standard values for these materials were obtained from (Jochum and others, 2014; 2011). The reference material MAPS-4 was analyzed throughout the session for drift. The ablation signals were screened visually for heterogeneities such as micro-inclusions or zoning.