This study evaluated the effects of organic agriculture manuring systems on carrot (Daucus carota) root morphology and sugar and polyacetylene content. Carrots were harvested three times per season 2006–2007 in a long-term field experiment at Skilleby research farm, Sweden. The effects of pelleted chicken manure, fresh farmyard manure and composted farmyard manure (COM) were compared against control plots left unmanured since the field experiment started in 1991. The carrots were analyzed for root size, root shape, amount of soluble sugars and amount of falcarinol-type polyacetylenes. Differences between manuring systems were found to be smaller than the variation between harvest years and harvest occasions, probably due to the grass-clover ley included in the crop rotation system. On an average for the six harvests, manuring with COM increased root length by 6% compared with fertilizing with pelleted chicken manure. Carrots fertilized with pelleted chicken manure also had 6–7% lower total soluble sugar content than carrots manured with 50 t ha−1 of composted or fresh manure. The falcarinol to total falcarinol-type polyacetylenes ratio was 15.4% in carrots manured with 50 t ha−1 of composted or fresh manure and 14.7% in carrots fertilized with pelleted chicken manure. Seasonal fluctuations in falcarinol-type polyacetylenes were more pronounced in carrots manured with fresh or composted manure than in carrots fertilized with pelleted chicken manure. The results suggest that manuring organic carrots with compost may be the most beneficial strategy, at least in systems where fertilizer is applied only once per crop rotation, whether directly to the carrot crop or in the preceding crop.