Background: The Indonesian government faces a dilemma of promoting fish consumption for its health benefits and to ease food insecurity, while at the same time seeking effective approaches to reduce the high levels of marine pollution. However, the factors associated with fish consumption in the face of persistent high levels of marine pollution are not well elucidated in the literature. Objectives: This was an explorative study to investigate the sociodemographic factors related to fish consumption and to understand the perspectives of expert informants on marine pollution and its impact on fish quality and availability in Indonesia. Methods: We characterized fish consumption among respondents aged 15 years and older in the fifth wave of the Indonesian Family Life Survey (n = 31,032), based on their sociodemographic profiles, and developed multinomial regression models to assess the relationship between respondents’ sociodemographic profiles and quintiles of fish consumption. We also conducted in-depth interviews on fish consumption and marine pollution with key informants from Indonesia (n = 27). We then used a convergent mixed-methods design to synthesize the results of both datasets. Results: Fish was the most frequently consumed animal-source food reported by survey respondents: 2.8 (±2.6) days/week. More younger respondents (15–19 years) reported relatively lower consumption of fish (9.3% in Q1 versus 5.9% in Q5) compared to respondents 50 years and older (37% in Q1 versus 39.9% in Q5; p < 0.01). When classified by region, more respondents from the Java region reported lower consumption of fish (86.5% in Q1 versus 53% in Q5; p < 0.01). Key-informants’ perspectives corroborated the survey results by indicating that the younger generation tends not to want to consume fish; informants expanded the survey results by suggesting that fish is scarce in the Java region due to high levels of marine pollution. Informants further implied that there is low awareness about the impact of marine pollution on fish quality among most of the Indonesian population. Conclusion: Evidence from both data sources converge on differential preference for fish consumption by age group. Informants’ perspectives also link marine pollution to fish scarcity, which poses a threat to food security among low-income Indonesians and to human health globally. More studies are needed to corroborate our findings and inform policy guidelines to reduce marine pollution while promoting fish consumption in Indonesia.