Background/Objectives: Obesity-related insulin resistance leads to the development of type 2 diabetes mellitus (T2DM); however, the pathophysiology of these metabolic alterations remains incompletely understood. This study aimed to characterize the lipidomic alterations during obesity–insulin resistance–T2DM progression in a high-sugar diet (HSD) model. Methods: Fruit flies were fed either a standard diet (SD) or an HSD and monitored across a 14-day period. Metabolic phenotyping and lipidomic profiling were conducted during the experiment. Results: After two days of HSD, fruit flies exhibited an obesity phenotype (50% increase in triglyceride content) and insulin resistance (hyperglycemia and insulin overexpression), progressing to an early T2DM-like state (increased triglycerides, hyperglycemia, and normal insulin expression) from days 4 to 6, and finally to a late T2DM-like phenotype (increased triglycerides, hyperglycemia, and insulin down-regulation) from days 8 to 14. Multivariate analyses indicated an altered lipidome profile in HSD-fed fruit flies from day 2 until the end of the experiment. Fatty acids and phosphatidylethanolamines (PEs) containing 16:0, 16:1, and 18:1 acyl chains were significantly altered during the development of obesity-related insulin resistance and early T2DM-like state (days 2 to 6); whereas palmitic acid and oleic acid-LysoPE alterations were associated with the onset and progression of obesity-related T2DM-like state (days 4 to 14). Conclusions: The progression from obesity-related insulin resistance to a T2DM-like state in an HSD-fed D. melanogaster model is accompanied by distinct lipidomic signatures involving 16- and 18-carbon fatty acid derivatives. These findings provide insight into potential biomarkers and mechanistic pathways in the early pathogenesis of T2DM.