The aims of the study were to determine the long-term effects of dietary supplementation with microalgae (SCIM) on milk and blood fatty acid (FA) composition and reproductive hormones in early lactation dairy cows. Sixty Holstein–Friesian dairy cows (30 per treatment) were unsupplemented (Control) or supplemented with 100 g of SCIM (Schizochytrium limacinum sp.) per cow per day from 25 ± 0.5 d post-partum for 98 d. Intake and milk yield were recorded daily, with milk samples collected at weeks 0, 1, 2, 4, 8 and 14, and blood samples collected from 12 representative pairs per treatment at weeks 0, 2, 4, 8, and 14 for subsequent analysis of FA, β-hydroxybutyrate, non-esterified fatty acids and glucose. At 33 ± 0.9 d postpartum the oestrus cycle of 24 cows (12 per treatment) were synchronized and plasma 13,14-dihydro-15-keto PGF2α (PGFM) concentrations determined following an oxytocin challenge. Data were analysed by repeated measures analysis of variance. There was no effect of treatment on dry matter intake, milk yield or milk fat content, with mean values across treatments of 22.1 and 40.6, and 37.2 g/kg respectively. Milk fat concentration of C22:6 n-3 increased rapidly in cows receiving SCIM, reaching a maximum of 0.38 g/100 g FA by week 14. Similarly, blood concentration of C22:6 n-3 increased to 1.6 g/100 g FA by week 14 in cows fed SCIM. There was no effect of treatment on plasma metabolites, but plasma glucose was lower in cows fed SCIM compared to the Control at week 2, and higher in week 8. There was no effect of treatment on peak plasma PGFM concentration or area under the curve. It is concluded that feeding SCIM rapidly increases blood and milk concentrations of C22:6 n-3 which are maintained over time, but does not improve plasma PGFM in dairy cows.