Context. The Rosetta encounter with comet 67P/Churyumov-Gerasimenko provides a unique opportunity for an in situ, up-close investigation of ion-neutral chemistry in the coma of a weakly outgassing comet far from the Sun. Aims. Observations of primary and secondary ions and modeling are used to investigate the role of ion-neutral chemistry within the thin coma. Methods. Observations from late October through mid-December 2014 show the continuous presence of the solar wind 30 km from the comet nucleus. These and other observations indicate that there is no contact surface and the solar wind has direct access to the nucleus. On several occasions during this time period, the Rosetta/ROSINA/Double Focusing Mass Spectrometer measured the low-energy ion composition in the coma. Organic volatiles and water group ions and their breakup products (masses 14 through 19), CO + , and CO + 2 (masses 28 and 44) and other mass peaks (at masses 26, 27, and possibly 30) were observed. Secondary ions include H 3 O + and HCO + (masses 19 and 29). These secondary ions indicate ion-neutral chemistry in the thin coma of the comet. A relatively simple model is constructed to account for the low H 3 O + /H 2 O + and HCO + /CO + ratios observed in a water dominated coma. Results from this simple model are compared with results from models that include a more detailed chemical reaction network. Results. At low outgassing rates, predictions from the simple model agree with observations and with results from more complex models that include much more chemistry. At higher outgassing rates, the ion-neutral chemistry is still limited and high HCO + /CO + ratios are predicted and observed. However, at higher outgassing rates, the model predicts high H 3 O + /H 2 O + ratios and the observed ratios are often low. These low ratios may be the result of the highly heterogeneous nature of the coma, where CO and CO 2 number densities can exceed that of water.