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• Shrub encroachment promoted C and N accumulation in alpine meadow and alpine steppe. • Shrub encroachment increased herbaceous plant richness and aboveground biomass. • Microbe-derived soil carbon and nitrogen were also enhanced by shrub encroachment. • Mechanisms leading to SOC S and STN S accumulation varied between alpine meadow and alpine steppe. Shrub encroachment can significantly affect the ecosystem structure and functioning of alpine grasslands. However, little is known about how this phenomenon alters soil organic carbon stocks (SOC S) and soil nitrogen stocks (STN S) in different alpine grassland ecosystems within the same region. Here we addressed this research gap by investigating the SOC S and STN S of encroached and non-encroached plots in alpine meadow and alpine steppe ecosystems on the central Tibetan Plateau. We found that, in both ecosystems, shrub encroachment significantly increased herbaceous plant richness, diversity, and aboveground biomass, but more notably in alpine meadow. Conversely, shrub encroachment increased belowground plant biomass in alpine steppe but had the opposite effect in alpine meadow, where belowground biomass was four times lower at encroached than at non-encroached plots. Importantly, encroaching shrubs resulted in significantly higher SOC S and STN S in both ecosystems, with alpine steppe showing the greatest carbon and nitrogen gains. The shrub encroached plots had 34.24 % and 97.25 % higher carbon stocks and 70.87 % and 67.34 % higher nitrogen stocks than non-encroached plots at the alpine meadow and alpine steppe, respectively. Increases in carbon and nitrogen stocks occurred mostly at the 10–30 cm soil layer and were highly correlated with shrub-induced changes in the herbaceous community composition. Overall, our results indicated that (1) shrub encroachment promoted carbon and nitrogen accumulation in the soils of both alpine meadow and alpine steppe and (2) the degree of accumulation and the mechanisms behind these changes varied between the two alpine grasslands. Our findings advance the general understanding of the soil carbon and nitrogen dynamics in shrub‐encroached alpine grasslands and highlight the importance of investigating how this phenomenon affects different ecosystems within the same region. [ABSTRACT FROM AUTHOR]