Climate change in the Arctic is outpacing the global average and land-use is intensifying due to exploitation of previously inaccessible or unprofitable natural resources. A comprehensive understanding of how the joint effects of changing climate and productivity modify lake food web structure, biomass, trophic pyramid shape and abundance of physiologically essential biomolecules (omega-3 fatty acids) in the biotic community is lacking. We conducted a space-for-time study in 20 subarctic lakes spanning a climatic (+3.2 degrees C and precipitation: +30%) and chemical (dissolved organic carbon: +10 mg/L, total phosphorus: +45 mu g/L and total nitrogen: +1,000 mu g/L) gradient to test how temperature and productivity jointly affect the structure, biomass and community fatty acid content (eicosapentaenoic acid [EPA] and docosahexaenoic acid [DHA]) of whole food webs. Increasing temperature and productivity shifted lake communities towards dominance of warmer, murky-water-adapted taxa, with a general increase in the biomass of primary producers, and secondary and tertiary consumers, while primary invertebrate consumers did not show equally clear trends. This process altered various trophic pyramid structures towards an hour glass shape in the warmest and most productive lakes. Increasing temperature and productivity had negative fatty acid content trends (mg EPA + DHA/g dry weight) in primary producers and primary consumers, but not in secondary nor tertiary fish consumers. The massive biomass increment of fish led to increasing areal fatty acid content (kg EPA + DHA/ha) towards increasingly warmer, more productive lakes, but there were no significant trends in other trophic levels. Increasing temperature and productivity are shifting subarctic lake communities towards systems characterized by increasing dominance of cyanobacteria and cyprinid fish, although decreasing quality in terms of EPA + DHA content was observed only in phytoplankton, zooplankton and profundal benthos.