This dataset consists of surface underway measurements collected during container ship Jona Sophie SOOP cruises (EXPOCODEs 687B20190207, 687B20190210) in the coastal waters of North Africa, Strait of Gibraltar, and North Atlantic Ocean from 2019-02-07 to 2021-05-04. An automated underway seawater and low atmospheric CO2 molar fraction (xCO2) measurement system, developed by Craig Neill and commercialized by General Oceanics™, with additional sensors of temperature, salinity and oxygen, was installed inside the engine room of the JONA SOPHIE container ship (named as RENATE P before September 2021). The system combines an air and water equilibrator with an infrared analyzer for detection which produces comparable and high quality data sets (Pierrot et al., 2009). Measurements of xCO2 (ppm) in seawater with frequencies of 2–3 min were performed by extracting seawater from the ship's supply at flow rates greater than 60 Lmin–1 and passing it through a plexiglass equilibrator at flow rates ranging between 3 and 4 Lmin−1. The system also performs three xCO2 measurements in low atmosphere per hour used to compute atmospheric CO2 content. In both cases, a non-dispersive infrared analyzer built by LICOR® (initially the 6262 model and after October 2019, a 7000 model) were used for the detection of xCO2. Due to technical problems with the measurement equipment aboard the VOS, no temperature, salinity or xCO2 measurements were obtained during March 2019 (problems with water intake), during the second half of August 2019 (problems with LICOR flow) and on a limited number of return journeys from the port of Barcelona. The dataset allows the study of spatio-temporal variability in the distribution of surface ocean CO2 in the Strait of Gibraltar with unprecedented high resolution.