Industrial fermentation procedures involve the mixing of multiple phases (solid, liquid, gaseous), where the interfacial area between the phases (air bubbles, oil drops and aqueous medium) determines the nutrients transfer and hence the performance of the culture. Interactions between phases occur, giving rise to the formation of complex structures containing air bubbles and small drops from the aqueous phase, trapped in oil drops (water-in-oil-in-water). A two-dimensional observation of this phenomenon may lead to an erroneous determination of the phenomena occurring since bubbles and droplets coming from different focal planes may appear overlapped. In the present work, an original strategy to solve this problem is described. Micro-stereoscopic on-line image acquisition techniques have been used, so as to obtain accurate images from the cultures for further three-dimensional analysis. Using this methodology, the three-dimensional spatial position of the trapped bubbles and droplets moving at high speed can be calculated in order to determine their relative concentration. To evaluate the accuracy of this technique, the results obtained with our system have been compared with those obtained by an expert. An agreement of 95% was achieved. Also, this technique was able to evaluate 14% more bubbles and droplets corresponding to overlaps that the expert was not able to discern in non-stereoscopic images.