Context. Isotopic abundances in comets are key to understanding and reconstructing the history and origin of material in the Solar System. Data for deuterium-to-hydrogen (D/H) ratios in water are available for several comets. However, no long-term studies of the D/H ratio in water of a comet during its passage around the Sun have been reported thus far. Linear alkanes are important organic molecules that have been found on several Solar System bodies, including comets. To date, the processes of their deuteration are still poorly understood, only the upper limits of isotopic ratios for D/H and 13C/12C in linear alkanes are currently available. Aims. The aim of this work is to carry out a detailed analysis of the D/H ratio in water as a function of cometary activity and spacecraft location above the nucleus. In addition, a first determination of the D/H and 13C/12C ratios in the first four linear alkanes, namely, methane (CH4), ethane (C2H6), propane (C3H8), and butane (C4H10) in the coma of 67P/Churyumov-Gerasimenko is provided. Methods. We analysed in situ measurements from the Rosetta/ROSINA Double Focusing Mass Spectrometer (DFMS). Results. The D/H ratio from HDO/H2O and the 16O/17O ratio from H216O/H217O did not change during 67P’s passage around the Sun between 2014 and 2016. All D/H ratio measurements were compatible within 1σ, with the mean value of 5.01 × 10−4 and its relative variation of 2.0%. This suggests that the D/H ratio in 67P’s coma is independent of heliocentric distance, level of cometary activity, or spacecraft location with respect to the nucleus. Additionally, the 16O/17O ratio could be determined with a higher accuracy than previously possible, yielding a value of 2347 with a relative variation of 2.3%. For the alkanes, the D/H ratio is between 4.1 and 4.8 times higher than in H2O, while the 13C/12C ratio is compatible, within the uncertainties, with the available data for other Solar System objects. The relatively high D/H ratio in alkanes is in line with results for other cometary organic molecules and it suggests that these organics may be inherited from the presolar molecular cloud from which the Solar System formed.