The innate and adaptive immune systems, though often studied separately, interact deeply and respond to stimuli simultaneously, with leukocytes displaying a range of pro- to anti-inflammatory phenotypes. This protocol details a procedure for characterizing murine innate and adaptive immune phenotypes using a 40-color full-spectral flow cytometry panel. We describe steps for organ collection, sample preparation, immunofluorescent staining, and acquisition to reproducibly and cost-effectively study tissue-resident leukocytes, their subpopulations, and inflammatory status in various organs.