Economical dispatch of power is no more a sole concern for the utilities. Rather, the utilities focus on the reduction of toxic gases to the atmosphere that is emitted due to the maximum utilization of conventional fossil-fuelled generators in order to meet the surging demand for electricity. This can be done by involving renewable energy sources (RES) to generate clean power completing the depletion in the availability of fossil fuels. This paper performs dynamic economic emission dispatch (DEED) on two islanded microgrid systems with and without the involvement of RES. Two methods of DEED viz. price-penalty factor (PPF) method and fractional programming (FP) method are used to perform DEED for both the microgrid test systems and a comparative analysis between them is made based on the lest emission of harmful and toxic gases in the atmosphere. A novel probabilistic (pCSA-JAYA) algorithm is used as the optimization tool for the study. Numerical results manifest the fact that FP method of solving DEED emits less toxic gases to the atmosphere compared to the PPF method. Also proposed pCSA-JAYA outperformed a long list of algorithms from recent literature in consistently providing a better and superior solution.