Many symbionts provide nutrients to their host and/or affect its phenotypic plasticity. Such symbiont effects on host resource acquisition and allocation are often simultaneous and difficult to disentangle. Here we partitioned symbiont effects on host resource acquisition and allocation using a new framework based on the analysis of a well-established trade-off between host fitness components. This framework was used to analyze the effect of symbiotic yeast on the larval development of Drosophila larvae in field-realistic conditions. The screening of eighteen yeast fresh isolates showed they had similar effects on the resource acquisition in Drosophila melanogaster, D. simulans and D. suzukii but species-specific effects on resource allocation between either larval development speed or adult size. These differences shed light on the ecology of Drosophila flies and illustrate why distinguishing between these qualitatively different effects of microorganisms on hosts is essential to understand and predict symbiosis evolution.