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Background  Lignocellulosic ethanol has a high potential as renewable energy source. In recent years, much research effort has been spent to optimize parameters involved in the production process. Despite that, there is still a lack of comprehensive studies on process integration. Single parameters and process configurations are, however, heavily interrelated and can affect the overall process efficiency in a multitude of ways. Here, we present an integrative approach for bioethanol production from wheat straw at a representative laboratory scale using a separate hydrolysis and co-fermentation (SHCF) process. The process does not rely on commercial (hemi-) cellulases but includes enzyme production through  Hypocrea jecorina  (formerly  Trichoderma reesei ) on the pre-treated feedstock as key unit operation. Hydrolysis reactions are run with high solid loadings of 15% dry mass pre-treated wheat straw (DM WS), and hydrolyzates are utilized without detoxification for mixed glucose-xylose fermentation with the genetically and evolutionary engineered  Saccharomyces cerevisiae  strain IBB10B05.    Results  Process configurations of unit operations in the benchtop SHCF were varied and evaluated with respect to the overall process ethanol yield ( Y  Ethanol-Process ). The highest  Y  Ethanol-Process  of 71.2 g ethanol per kg raw material was reached when fungal fermentations were run as batch, and the hydrolysis reaction was done with an enzyme loading of 30 filter paper units (FPU)/g DM WS . 1.7 ± 0.1 FPU/mL were produced, glucose and xylose were released with a conversion efficiency of 67% and 95%, respectively, and strain IBB10B05 showed an ethanol yield of 0.4 g/g Glc + Xyl  in 15% hydrolyzate fermentations. Based on the detailed process analysis, it was further possible to identify the enzyme yield, the glucose conversion efficiency, and the mass losses between the unit operations as key process parameters, exhibiting a major influence on  Y  Ethanol-Process .    Conclusions   Y  Ethanol-Process  is a measure for the efficiency of the lignocellulose-to-bioethanol process. Based on mass balance analysis, the correlations between single process parameters and  Y  Ethanol-Process  were elucidated. The optimized laboratory scale SHCF process showed efficiencies similar to pilot scale plants. The herein presented process analysis can serve as effective and simple tool to identify key process parameters, bottlenecks, and future optimization targets.    Electronic supplementary material  The online version of this article (doi:10.1186/s13068-015-0232-0) contains supplementary material, which is available to authorized users.

From wheat straw to bioethanol: integrative analysis of a separate hydrolysis and co-fermentation process with implemented enzyme production