This study was conducted in the Middle Branch of Bue Marino Cave (Sardinia, Italy) to reconstruct paleoecological conditions during the Holocene through microfaunal proxies in seven surface sediment samples and a short sediment core (BMD-2018, 18 cm), all collected in 2018 and another core sampled in 2021 (BMD-2021, 28 cm). The first attempt at dating cave sediment through luminescence was conducted on BMD-2021; the derived age was 6.04 ± 0.47 ka at 18 cm depth. Although continuous sedimentation and constant rates are not probable in the cave, this indicates that the sedimentary record dates to the early times after the Holocene flooding of the cave by the sea. Benthic foraminifera and grain size were analyzed in all surface samples and core BMD-2018, while only benthic foraminifera were studied in BMD-2021. The recent foraminiferal assemblages, studied from an ecological point of view, were applied as modern analog to reconstruct the paleoecological conditions in sediment cores. Significant changes in the sedimentary environment were excluded; the two cores showed a similar foraminiferal turnover at a similar depth, from an older assemblage with prevailing indifferent Ammonia inflata to a younger one with prevailing opportunist Eggerelloides advena. This turnover was attributed to changes in the amount and/or quality of available nutrients. Based on these results, this event is likely related to possibly attributable to the effects of climate changes that occurred in the Holocene. However, more extensive studies are necessary to better understand the effects of the climatic/environmental events in the Late-Holocene in the caves. Although it represents a first attempt at paleoenvironmental reconstruction based on sediments from a Mediterranean marine cave, this study demonstrated that benthic foraminifera are refined paleoenvironmental proxies and that the integrated approach with the luminescence dating produces reliable results for studying the effects of global changes in these environments.