Effective breeding requires multiplying desired genotypes, keeping them at a convenient location to perform crosses more efficiently, and building orchards to generate material for reforestation. While some of these aims can be achieved by conventional grafting involving only rootstock and scion, topgrafting is known to deliver all in a shorter time span. In this study, Scots pine scions were grafted onto the upper and lower tree crowns in two clonal archives with the aim of inducing early female and male strobili production, respectively. Their survival rates and strobili production were analyzed with generalized linear mixed models. Survival was low (14%) to moderate (41%), and mainly affected by the topgraft genotype, interstock genotype, crown position and weather conditions in connection with the grafting procedure. Survival was not affected by the cardinal position in the crown (south or north). Male flowering was ample three years after grafting and reached 56% in the first year among live scions, increasing to 62 and 59% in consecutive years. Female flowering was scarce and was 9% at first, later increasing to 26 and 20% of living scions but was strongly affected by the topgraft genotype. In one subset of scions, female flowering was observed 1 year after grafting. Overall, flowering success was mainly affected by the topgraft and interstock genotypes, and secondary growth of scions. This is one of few reports on topgrafting in functional Scots pine clonal archives.