Urban centers worldwide are facing escalating challenges due to motorized road transport, creating an urgent need to promote active modes. This paper aims to investigate the factors influencing Athenians’ choices towards active commuting options, specifically bicycles and scooters, for work-related travel, and assesses the acceptance of the “Bike to Work” scheme. A questionnaire using the stated preference methodology was developed, featuring twelve scenarios with and without cycling infrastructure, and varying factors like travel time, cost, and health benefits. Two multinomial logistic regression models analyzed preferences for active commuting under different cycling infrastructural conditions, and a binomial logistic regression model examined the acceptance of the scheme and its influencing factors. The findings indicate that health benefits significantly boost preferences for bicycles and e-scooters, while adequate cycling infrastructure mitigates the effects of longer commute times. Socio-demographic factors, such as age and profession, also influence commuting choices, highlighting the need for targeted interventions. The results underscore the importance of fostering positive perceptions of cycling sustainability and addressing safety concerns to enhance participation in the “Bike to Work” scheme. Policymakers should prioritize developing comprehensive cycling networks and implementing educational initiatives to promote active commuting, making urban transportation systems more sustainable and inclusive.