Surface underway physicochemical measurements were performed in open-ocean and archipelagic coastal waters of the Macaronesia region during the POS533 cruise (from February 28 to March 19, 2019) on board the RV Poseidon. The Macaronesia region show a high variability due to its location in a coupling area between the Canary Upwelling System along the Northwest African coast and the oligotrophic open-ocean waters of the Northeast Atlantic subtropical gyre and the influence of the island interaction with the Canary Current. Thus is a key zone in terms of CO2 distribution, natural and anthropogenic carbon inventory and air-sea exchange and requires the develop of regional-scale field studies. The autonomous monitoring was carried out through the vessel track mainly downwind in the archipelagos of Cape Verde, Canary and Madeira and through the latitudinal transects that connect them. The obtained dataset includes sea surface temperature (SST), salinity (SSS) and pH values with a temporal frequency of data collection of 5 minutes. The SST and SSS were monitored by using a SeaCat SBE21 termosalinograph placed at the same location of the seawater immersed pump (main seawater intake of the RV Poseidon) with an accuracy of 0.01 ºC and 0.001, respectively. A spectrophotometric pH sensor (SP101-SM) developed by the QUIMA group (IOCAG-ULPGC) and SensorLab (González-Dávila et al., 2014; 2016) and based on the method described by Clayton and Byrne (1993) was run in continuous and used for the surface pH monitoring. The SP101-SM pH sensor uses 4 wavelengths analysis for the m-cresol purple, includes auto-cleaning steps, performs a blank for pH calculation immediately after the dye injection and removes any dye effect in each pH reading (the accuracy with respect to a TRIS seawater buffer was ±0.002 units). These in-situ collected data improve the knowledge about the biogeochemistry in eastern boundary transitional areas and allows a better understanding of the role in the climate change of archipelagic waters, coastal regions and island/continental shelves. The provided datasets can be used in further biogeochemical studies in the Macaronesia region and in the entire Northeast Atlantic. The monitoring and data collection received fundings from the Atmosphere-Ocean-Islands-Biogeochemical interactions in the Macaronesian Archipelagos of Cabo Verde, the Canaries and Madeira project (AIMAC project) and the European Union's Horizon 2020 research and innovation program under grant agreement Nº 820989 (COMFORT project). In this case, the measurements complemented those done for iron study (Santana-Casiano and Quack, 2021).