Absolute sea-level rise has become an important topic globally due to climate change. In addition, relative sea-level rise due to the vertical land motion in coastal areas can have a big societal impact. Vertical land motion (VLM) in Southeast Asia includes a tectonically induced component: uplift and subsidence in plate boundary zones where both Peninsular and East Malaysia are located. In this paper, the relative sea-level trends and (seismic cycle-induced) temporal changes across Malaysia were investigated. To do so, the data (1984–2019) from 21 tide gauges were analyzed, along with a subset (1994–2021) of nearby Malaysian GNSS stations. Changes in absolute sea level (ASL) at these locations (1992–2021) were also estimated from satellite altimetry data. As a first for Peninsular and East Malaysia, the combination ASL minus VLM was robustly used to validate relative sea-level rise from tide-gauge data and provide relative sea-level trend estimates based on a common data period of 25+ years. A good match between both the remote and in situ sea-level rise estimations was observed, especially for Peninsular Malaysia (differences < 1 mm/year), when split trends were estimated from the tide gauges and GNSS time series to distinguish between the different VLM regimes that exist due to the 2004 Sumatra–Andaman megathrust earthquake. As in the south of Thailand, post-seismic-induced negative VLM has increased relative sea-level rise by 2–3 mm/year along the Andaman Sea and Malacca Strait coastlines since 2005. For East Malaysia, the validation shows higher differences (bias of 2–3 mm/year), but this poorer match is significantly improved by either not including data after 1 January 2014 or applying a generic jump to all East Malay tide gauges from that date onwards. Overall, the present relative sea-level trends range from 4 to 6 mm/year for Malaysia with a few regions showing up to 9 mm/year due to human-induced land subsidence.