The Sinú-San Jacinto Belt (SSJB) is a set of folded and faulted onshore deposits in the Caribbean region of Colombia near the tectonic boundary of the Caribbean and South American plates. Previous studies relied on biostratigraphic data from mollusks, benthic and subsequently planktonic foraminifera to establish a tectonostratigraphic framework from the Late Cretaceous to Pleistocene for these deposits. In this study, we collected over 10 years of new biostratigraphic information from calcareous nannofossils, an oceanic micropaleontological group with well-calibrated biostratigraphy, providing us the opportunity to evaluate the prior age determinations and to refine the tectonostratigraphic framework of these deposits. We found that the recovery of calcareous nannofossils varied, observing that large barren intervals affected chronostratigraphic constrains on southwestern deposits accumulated in nearshore environments. However, despite this limitation, the occurrences of biostratigraphic markers allowed us to establish that lower Eocene, upper Eocene, Oligocene, Lower Miocene and Upper Miocene deposits occur in different localities of the belt, whereas Upper Cretaceous and upper Paleocene are scarcer. Our results support the previous chronostratigraphic framework, but also indicate that the duration and origin of the hiatuses can vary with location in the belt, complicating regional correlations of the tectonostratigraphic boundaries. We suggest that integrated biostratigraphic and sedimentologic studies from additional cored sections and outcrops would help to understand the polygenetic origin of unconformities that affect the stratigraphic record in the Caribbean region of Colombia.