Successful ecological engineering of bioprocesses implies the ability to steer microbial community assembly towards structures with a desirable performance. To test experimentally how substrate complexity and inoculum characteristics affect community assembly, we used anaerobic digesters in which methane production is a measurable proxy of ecosystem function. We used an experimental set-up with 30 small-scale (180 ml) anaerobic digesters operated in continuous mode. The experiment was conducted using five different base inocula. 15 reactors were started with mixtures of four of them, while the remaining 15 reactors were started using the individual base inocula. Digesters were fed with one of three different synthetic substrates varying in chemical complexity, (i.e., diversity of chemical bonds and polymer length). This experimental design allowed us to simultaneously test the effects of substrate complexity and community mixing on the community function. Mixed communities fed with the most complex substrate shared high similarity to all of the four communities derived from the individual base inocula. When grown on simpler substrates, we observed lower similarities to the corresponding base inocula. The ability of the mixed communities to incorporate traces of all base inocula into a novel, coalesced community increased with increasing substrate complexity. Overall, ecosystem performance did not significantly correlate with community coalescence, even though specific coalesced communities showed considerably different performance than the average. Our results indicate that mixing and the resulting community coalescence may under certain conditions improve ecosystem function but cannot be considered a general strategy to achieve performance improvements.