Little is known about how citizens perceive the transition towards a bio-based economy (BBE), despite the fact that they are one of the most important actors in this transition. Citizens' perceptions of bio-based innovations can support policy-makers to improve the quality of decision-making and the bio-based industry to develop innovations. This study explores Dutch citizens' arguments for and against three selected bio-based innovations: bioplastics, bio-jetfuels and small-scale bio-refineries. Randomly selected Dutch citizens were consulted in seven focus groups discussions (n. = 57). Results show that participants generally favor the contribution of bio-based technologies to economic growth and sustainability, but also mentioned several negative effects, such as high costs, food shortages or deforestation. In forming their opinion, citizens carefully weigh pros and cons of bio-based technologies from the perspective of their own interests and context, and this varies per bio-based technology. Their acceptance and support towards bio-based technologies increases when they feel more engaged with these technologies, and becomes even stronger when they identify opportunities for direct personal benefits, as in the case of the small-scale bio-refinery. This acceptance and support reduces if another important value is threatened (e.g. accessible mobility in the case of bio-jetfuels). Reliable information on both the advantages and disadvantages of bio-based technologies, coming from a neutral and independent body, is necessary in order for citizens to make their own judgments.