After pollination outdoors, individual bilberry plants from two Northern and two Southern clones were studied for climatic effects on berry yield and quality in a controlled phytotrone experiment at 12 and 18 °C. At each temperature, the following light treatments were tested: (1) 12 h natural light, (2) 24 h natural light, and (3) 24 h natural light plus red light. The first experimental year there was no difference in yield between temperatures; however, the second experimental year the berry yields was significantly higher at 18 °C. Berry ripening was faster in the Northern than in the Southern clones at 12 °C. Northern clones also showed significantly higher contents of total anthocyanins, all measured anthocyanin derivatives, total phenolics, malic acid and sucrose. Metabolic profiling revealed higher levels of flavanols, hydroxycinnamic acids, quinic acid and carbohydrates at 12 °C.