Three disaggregation methods, i.e. Calgon, acetic acid and electric pulse fragmentation (EPF), have been applied to a range of heavily lithified, carbonate-rich sedimentary rock samples of Paleogene age. Samples are predominantly from the carbonate-rich, shallow water domain (<250 m palaeo-water depth) of Tanzania, Malta and the United Arab Emirates (Paleogene Tethys Ocean). The effectiveness and efficiency of each method has been compared, in addition to the preservation of the resultant liberated microfossil material (primarily larger foraminifera; LF). Of the three methods, the most efficient and effective was EPF, which liberated the largest number of LF in a very short processing time and resulted in the best preservation. Samples with calcitic, silicic, and clay matrices and cements were successfully disaggregated using EPF. In this study, recovered microfossils were largely >500 µm, suggesting this technique may be more appropriate for liberating larger microfossils (e.g. LFs); however, we discuss nuances to the method that would allow for more effective recovery of smaller microfossil specimens. The more traditional acetic acid method was also able to disaggregate a number of the samples; however, preservation of the LF was compromised. We suggest a best-practice methodology for implementing EPF in micropalaeontological studies.