A variety of methods and arrangements for controlling the exhaust gas temperature of a lean burn, skip fire controlled internal combustion engine are described. In one aspect, an engine controller includes an aftertreatment system monitor and a firing timing determination unit. The aftertreatment monitor obtains data relating to a temperature of one or more aftertreatment elements, such as a catalytic converter. Based at least partly on this data, the firing timing determination unit generates a firing sequence for operating the engine in a skip fire manner such that the temperature of the aftertreatment element is controlled within its effective operating range.