The study aimed to evaluate the sustainability of a multi-component education (ABC-HEat) program related to healthy nutrition and lifestyle after three months and nine months and to assess the socioeconomic context in improving teenage nutrition knowledge. The study was designed as a clustered, controlled, education-based intervention. A sample was chosen and allocated into either an educated group (under intervention) or a control group (outside of intervention). The study covered 464 11–12-year-old students (educated/control 319/145). In the educated group, data were collected three times: before education, after three months and after nine months to measure the short- and the long-term effects of education, respectively. In the control group, data were collected in parallel. Changes in nutrition knowledge score (NKS, points) by sex, residence, family affluence scale (FAS) were the main outcome measures. The increase in the NKS was significantly higher in the educated group than in the control group—three months after education on average by 1.4 to 2.7 points (all p < 0.001) in the total sample and all subgroups, and nine months after education in rural residents by 2.2 points (p < 0.001) and in the total sample by 0.4 (p < 0.05). In the educated group, the chance of no increase in the NKS was higher in urban than rural residents after three months and nine months (adjusted odds ratios [OR] and 95% Confidence Intervals [95% CI]: 3.63, 1.80–7.31 and 2.99, 1.60–5.59, respectively, both p < 0.001) using the increase in the NKS by ≥4 points as a reference. The multi-component education program improved the nutrition knowledge of teenagers in the short term regardless of socioeconomic variables, but in the long term this effect was visible only in rural residents. It suggests that a special path of nutrition education addressed to urban teens may be required.