Amyloidosis is a shared name for several rare, complex and serious diseases caused by extra-cellular deposits of different misfolded proteins. Accurate characterization of the amyloid protein is essential for patient care. Immunoelectron microscopy (IEM) and laser microdissection followed by tandem mass spectrometry (LMD-MS) are new gold standards for molecular subtyping. Both methods perform superiorly to immunohistochemistry, but their complementarities, strengths and weaknesses across amyloid subtypes and organ biopsy origin remain undefined. Therefore, we performed a retrospective study of 106 Congo Red positive biopsies from different involved organs; heart, kidney, lung, gut mucosa, skin and bone marrow. IEM, performed with gold-labelled antibodies against kappa light chains, lambda light chains, transthyretin and amyloid A, identified specific staining of amyloid fibrils in 91.6%; in six biopsies amyloid fibrils were not identified, and in two, the fibril subtype could not be established. LMD-MS identified amyloid protein signature in 98.1%, but in nine the amyloid protein could not be clearly identified. MS identified protein subtype in 89.6%. Corresponding specificities ranged at organ level from 94–100%. Concordance was 89.6–100% for different amyloid subtypes. Importantly, combined use of both methods increased the diagnostic classification to 100%. Some variety in performances at organ level was observed.