Stable isotopes of benthic foraminifera have widely been applied in micropalaeontological research to understand vital effects in foraminifera. Isotopic fractionations are mainly controlled by ontogeny, bottom/pore water chemistry, habitat preference, kinetic effect and respiration. Discontinuous abundance of a species for isotopic analysis has forced us to select multiple species from down-core samples. Thus standardisation factors are required to convert isotopic values of one species with respect to other species. The present study is pursued on isotopic values of different pairs of benthic foraminifera from the Krishna–Godavari basin and Peru offshore to understand habitat-wise isotopic variation and estimation of isotopic correction factors for the paired species (Cibicides wuellerstorfi–Bulimina marginata, Ammonia spp.–Loxostomum amygdalaeformis and Bolivina seminuda–Nonionella auris). Infaunal species (B. marginata, Ammonia spp. and N. auris) show a lighter carbon isotopic excursion with respect to the epifaunal to shallow infaunal forms (C. wuellerstorfi, L. amygdalaeformis and B. seminuda). These lighter δ13C values are related to utilisation of CO2 produced by anaerobic remineralisation of organic matter. However, enrichment of δ18O for the deeper microhabitat (bearing lower pH and decreased CO32−) is only recorded in case of B. marginata. It is reverse in case of N. auris and related to utilisation of respiratory CO2 and internal dissolve inorganic carbon pool. Estimation of interspecies isotopic correction factors for the species pairs (δ13C of C. wuellerstorfi–B. marginata, L. amygdalaeformis–Ammonia spp., N. auris–B. seminuda) and δ18O of C. wuellerstorfi–B. marginata are statistically reliable and may be used in palaeoecological studies.