The maximizing emission reductions and economic savings simulator (MERESS) is an optimization tool that evaluates novel strategies for installing and operating combined heat and power (CHP) fuel cell systems (FCSs) in buildings. This article discusses the deployment of MERESS to show illustrative results for a California campus town and, based on these results, makes recommendations for further installations of FCSs to reduce greenhouse gas (GHG) emissions. MERESS is used to evaluate one of the most challenging FCS types to use for GHG reductions, the phosphoric acid fuel cell (PAFC) system. These PAFC systems are tested against a base case of a CHP combined cycle gas turbine (CCGT). Model results show that three competing goals (GHG emission reductions, cost savings to building owners, and FCS manufacturer sales revenue) are best achieved with different strategies but that all three goals can be met reasonably with a single approach. According to MERESS, relative to a base case of only a CHP CCGT providing heat and electricity with no FCSs, the town achieves the highest (1) GHG emission reductions, (2) cost savings to building owners, and (3) FCS manufacturer sales revenue each with three different operating strategies, under a scenario of full incentives and a $100/tonne carbon dioxide (CO2) tax (scenario D). The town achieves its maximum CO2 emission reduction, 37% relative to the base case with operating strategy V: stand-alone (SA) operation, no load following (NLF), and a fixed heat-to-power ratio (FHP) (SA, NLF, and FHP; scenario E). The town’s building owners gain the highest cost savings, 25% with strategy I: electrically and thermally networked (NW), electricity power load following (ELF), and a variable heat-to-power ratio (VHP) (NW, ELF, and VHP; scenario D). FCS manufacturers generally have the highest sales revenue with strategy III: NW, NLF with a FHP (NW, NLF, and FHP; scenarios B, C, and D). Strategies III and V are partly consistent with the way that FCS manufacturers design their systems today, primarily as NLF with a FHP. By contrast, strategy I is novel for the fuel cell industry, in particular, in its use of a VHP and thermal networking. Model results further demonstrate that FCS installations can be economical for building owners without any carbon tax or government incentives. Without any carbon tax or state and federal incentives (scenario A), strategy I is marginally economical with 3% energy cost savings but with a 29% reduction in CO2 emissions. Strategy I is the most economical strategy for building owners in all scenarios (scenarios A–D) and, at the same time, reasonably achieves other goals of large GHG emission reductions and high FCS manufacturer sales revenue. Although no particular building type stands out as consistently achieving the highest emission reductions and cost savings (scenarios B-2 and E-2), certain building load curves are clear winners. For example, buildings with load curves similar to Stanford’s Mudd chemistry building (a wet laboratory) achieve maximal cost savings (1.5% with full federal and state incentives but no carbon tax) and maximal CO2 emission reductions (32%) (scenarios B-2 and E-2). Finally, based on these results, this work makes recommendations for reducing GHG further through FCS deployment. (Part I of II articles discusses the motivation and key assumptions behind the MERESS model development.)