A multi-element graphite furnace atomic absorption spectrometry (GFAAS) method was elaborated and applied for the simultaneous determination of As, Cd, Cr, Cu, and Pb in various kinds of honey samples (acacia, floral, linden, rape, and milkweed) using the transversally heated graphite atomiser (THGA) with end-capped tubes and integrated graphite platforms (IGPs). For comparative GFAAS analysis, direct (without digestion) and indirect (with digestion in a microwave oven) sample preparation procedures were tested. The effects of several chemical modifiers, such as NH4H2PO4, NH4H2PO4–Mg(NO3)2, and Pd(NO3)2–Mg(NO3)2, were studied to obtain optimal pyrolysis and atomization conditions for the set of analytes studied. The most efficient modifier was proved to be the mixture of 5 μg Pd (applied as nitrate) plus 3 μg Mg(NO3)2, allowing the optimal 600 °C pyrolysis and 2300 °C atomization temperatures. To prevent the sputtering and foaming of the matrix during the drying and pyrolysis steps of the furnace heating program, the sample and modifier solutions (20 + 5 μl, respectively) were dispensed together onto the IGP of the THGA pre-heated at 80 °C.