Abstract Line Intercept Transects (LIT), Point Intercept Transects (PIT) and Photoquadrats (PQ) are the most common quantitative sampling techniques in modern and fossil coral reefs. Data from coral reefs obtained by the different methods are generally compared between various reef ages and localities. Quaternary reefs from warmer interglacial periods, which represent climate scenarios projected for the future, are particularly interesting for comparisons with modern reefs. Importantly, fossil reefs differ from modern reefs because they are diagenetically altered and time-averaged. While several studies have compared different quantitative methods in modern reefs, very few have dealt with the comparability among fossil and between fossil and modern reefs. Here, we compare LIT, PIT at 10, 20 and 50 cm intervals and PQ in two Pleistocene reef localities in Egypt. We find that alpha diversity, reef cover and community composition are dependent on the method. Results gained with plotless methods (LIT, PIT) differ strongly from results gained with plot methods (PQ). However, coral cover results are similar with LIT and PIT, and community composition is indistinguishable between the two, but alpha diversity depends on the interval used for PIT. We discuss the implications of our findings for comparing coral reefs of various ages and localities. We recommend surveying Pleistocene reefs with PIT at 20 cm intervals. This is because (1) alpha diversity is well captured, (2) the amount of time-averaging recorded by PIT is reduced compared to PQ, (3) the PIT results can be directly compared to reefs analysed by LIT and (4) the method is less time-consuming than LIT and PQ.