The present work demonstrates how drug-loaded mesoporous silica nanoparticles (MSNPs) can be prepared by a sequential flash nanoprecipitation (FNP) technique. A sequential FNP technique is developed relying on a combination of two multi-inlet vortex mixers (MIVM), by which a continuous process that involves the formation of micelle-based templates followed by an in situ formation of MSNPs is achieved. Moreover, a widely used biological nematicide, abamectin (Abm), is added during the formation of micelles, ultimately leading to Abm-loaded MSNPs with high encapsulation efficiency. The obtained Abm-loaded MSNPs show excellent stability and inhibition activity against the livability of Meloidogyne incognita. Importantly, the parameters of the resulting MSNPs, such as silica shell thickness and inner cavity size of MSNPs, can be easily controlled by tuning the compositions of the reactant streams. We believe that such a simple approach towards direct preparation of drug-loaded MSNPs would find promising up-scale applications in various fields, such as drug delivery, bioimaging, and formulation technology.