Several raw-data processing software for accelerometer-measured physical activity (PA) exist, but whether results agree has not been assessed. We examined the agreement between three different software for raw accelerometer data, and associated their results with cardiovascular risk. A cross-sectional analysis conducted between 2014 and 2017 in 2693 adults (53.4% female, 45-86 years) living in Lausanne, Switzerland was used. Participants wore the wrist-worn GENEActive accelerometer for 14 days. Data was processed with the GENEActiv manufacturer software, the Pampro package in Python and the GGIR package in R. For the latter, two sets of thresholds "White" and "MRC" defining levels of PA and two versions (1.5-9 and 1.11-1) for the "MRC" threshold were used. Cardiovascular risk was assessed using the SCORE risk score. Time spent (mins/day) in stationary, light, moderate and vigorous PA ranged from 633 (GGIR-MRC) to 1147 (Pampro); 93 (GGIR-White) to 196 (GGIR-MRC); 19 (GGIR-White) to 161 (GENEActiv) and 1 (GENEActiv) to 26 (Pampro), respectively. Spearman correlations between results ranged between 0.317 and 0.995, while concordance coefficients ranged between 0.035 and 0.968. With some exceptions, the line of perfect agreement was not in the 95% confidence interval of the Bland-Altman plots. Compliance to PA guidelines varied considerably: 99.8%, 98.7%, 76.3%, 72.6% and 50.2% for Pampro, GENEActiv, GGIR-MRC v.1.11-1, GGIR-MRC v.1.4-9 and GGIR-White, respectively. Cardiovascular risk decreased with increasing time spent in PA across most software packages. We found large differences in PA estimation between software and thresholds used, which makes comparability between studies challenging.