The burgeoning field of community genetics posits that genetic variation within species affects the structure and dynamics of associated communities and ecosystems. While many experiments support this hypothesis, we argue that the most commonly employed experimental design suffers from a fundamental flaw that might result in overestimating the importance of genetic variation. Specifically, most studies collect genotypes from a wide area but perform experiments in small common gardens. Since environmental and genetic variation typically increase with spatial scale, this mismatch in scale is predicted to artificially inflate estimates of the ecological importance of genetic effects. Furthermore, most existing studies have used study systems with particular ecological characteristics, which might further inflate the inferred importance of genetic variation. To critically examine this potential problem, we reanalyze previous studies in community genetics and show how current methods lead to biased conclusions. More specifically, while a growing body of literature shows that intraspecific genetic variation can have an effect, it does not accurately estimate its effect size. As a remedy to this bias, we propose an experimental design that can accurately quantify the importance of genetic and environmental variation in affecting communities and ecosystems.