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Introduction Socioeconomic deprivation is a major driver of multimorbidity (multiple long-term conditions, MLTCs) and polypharmacy in ageing populations. However, it is unclear how these inequalities evolve over time or influence early disease progression.Methods We conducted a population-based longitudinal study of 414 746 adults aged ≥51 years in Greater Glasgow and Clyde, Scotland, using linked administrative health records. Participants were followed at three timepoints (2016, 2019, 2021), with socioeconomic status defined by Scottish Index of Multiple Deprivation (SIMD) deciles. Outcomes included prevalence and progression of MLTCs and medication burden. Zero-inflated negative binomial (ZINB) models estimated the burden of disease and prescribing, and the likelihood of remaining disease-free or prescription-free, adjusted for age and sex.Results Multimorbidity and prescription burden increased over time across all groups. In 2021, 26.0% of individuals in the most deprived decile (SIMD1) had ≥5 conditions compared with 13.8% in the least deprived (SIMD10). From 2016 to 2021, individuals in SIMD10 were nearly 40% less likely to progress from a single condition to five or more (risk ratio=0.62 (0.60 to 0.63)) compared with SIMD1. ZINB models showed lower expected MLTC counts (incidence rate ratio (IRR)=0.59 (0.58 to 0.60)) and medication burden (IRR=0.91 (0.90 to 0.91)) in SIMD10, but also lower odds of remaining completely disease-free (OR=0.65 (0.63 to 0.68)) or prescription-free (OR=0.44 (0.41 to 0.47)). Findings were consistent in survivor-only sensitivity analyses (n=360 683).Conclusions Socioeconomic deprivation shapes disease and treatment trajectories from the earliest stages. Individuals in deprived areas experience faster accumulation of conditions and medications. These disparities are not explained by survival differences and highlight the need for equity-focused prevention, tailored care pathways and systems that address the social complexity of multimorbidity.