Alternative teaching methodologies are required for grade-9 students diagnosed with difficulties learning chemistry. This study examines the progress made in learning atomic structure by 11 Spanish Students Diagnosed with Learning Difficulties (SDLD, experimental group), including those with poor academic performance, specific learning difficulties in reading, writing, and mathematics, attention deficit hyperactivity disorder, and borderline intellectual disability according to the Spanish curriculum. The study was conducted as part of the Program for Improving Learning and Performance (PMAR) and utilized the game "Atomizados", specifically designed for this purpose. A written test on atomic structure was used to evaluate learning with three learning levels established (naïve, transitional, and informed). The findings indicate that 63.63% of the SDLD (experimental) achieved an informed learning level (understanding the internal structure of the atom) as a result of utilizing a generative learning strategy. The Mann-Whitney U test demonstrated that this learning was statistically significantly greater than that achieved by other students diagnosed with learning difficulties who did not use the game (SDLD control group). No significant differences were found between the SDLD experimental group and two other groups of grade-9 students with no learning difficulties (NSDLD control groups). However, differences were detected between SDLD (control) and NSDLD (control) in favor of the latter groups. The average for these control groups was a transitional level (identifying some elements of the atomic structure) in the best cases. SDLD (experimental) exhibited a very positive perception of the game's influence on learning chemistry, highlighting its attractiveness, interest, and potential for generating classroom participation.