Bacterial pathogens have the ability to secrete effector proteins to promote host cell invasion. The efficient analysis of the secretomes in close to wildtype cell systems is important to study the mechanisms of bacterial secretion efficiently at different levels. In particular the secretome analysis of bacteria that rely on rich media for optimal secretion may hamper analysis via modern sample preparation shotgun proteomics workflows due to higher degree of sample impurities. This is may be a reason for the low number of quantitative secretome investigations in such cells. We assessed the efficiency of different workflows and their amenability for secretome analysis including precipitation, SP3 and a combined, serial workflow. Using the model organism Pseudomonas aeruginosa, we found that, the combined TCA-SP3 strategy outperforms the other tested methods on all levels and proofed most efficient in the recovery of proteins related to the type III secretion system (T3SS), including all known effector proteins and secretion machinery components. Moreover, the serial workflows resulted in improved quantification accuracy using MS1 label-free quantification. Finally by monitoring the compositional changes of secretome samples over time we observed strong increase of the fraction made up by T3SS related proteins with parallel decrease of proteins not linked to T3SS. Our study shows how combining sample preparation procedures can lead to orthogonality in depleting impurities that result in better chromatographic peptide separation, and more efficient MS detection with improved quantification parameters.