In this study, in vitro-derived shoot tips of Eureka lemon (Citrus limon [L.] Burm. f. [‘Eureka’]) were encapsulated in various concentrations of sodium alginate (Na-alginate) (3%, 4%, and 5%) dissolved in liquid MS medium supplemented with 50 g l−1 sucrose + 10 mg l−1 BAP + 1 mg l−1 NAA (SA1); liquid MS medium supplemented with 50 g l−1 sucrose (SA2) and distilled water with 50 g l−1 sucrose (SA3). Encapsulated and non-encapsulated shoot tips were stored at 4°C for different storage periods (1-8 weeks). Alginate matrix of 4% Na-alginate and 100 mM CaCl2·2H2O was found to be suitable for the production of alginate beads. Shoots obtained by root induction were transferred to MS medium containing 5 mg l−1 IBA. Encapsulated shoot tips on SA1 treatment were viable (50%) after 3 weeks of cold storage while non-encapsulated shoot tips lost their viability completely after 3 weeks. Addition of MS nutrient and hormones to the alginate matrix significantly affected the regeneration of shoot tips. The survival rate of shoot tips encapsulated in SA1 after 4 weeks was 30% while that of encapsulated in SA2 was 20%. However, shoot tips encapsulated in SA3 lost their viability. Conversion frequencies of shoot tips encapsulated with SA1 in MS medium with hormones and without hormones were 60% and 30%, respectively, after 1 week. Thus, the current synthetic seed technology could be useful in large-scale propagation and short-term conservation of citrus.