Poly(oxymethylene) dimethyl ethers (OME) offer excellent fuel properties such as soot-free combustion and are discussed as potential diesel fuels. Formation of side products during their production, a crucial factor for the feasibility of the process, has been of minor consideration so far. This work investigates the formation of side products during the OME synthesis via a recently proposed route from methanol and concentrated aqueous formaldehyde solution over the acidic ion exchange resin Amberlyst 46 as heterogeneous catalyst. Batch experiments under elevated temperatures and pressures and long residence time are carried out. The kinetics of the formation of the side products trioxane, methyl formate, and formic acid are quantified and modeled. Implications for the process design are examined in process simulation studies. Some side products accumulate within the process, and thus, their removal is indispensible. Introducing a purge stream results in 2.7% loss of product at a reactor temperature of 343.15 K, which emphasizes the need for further investigations regarding side product formation under process conditions, advanced removal methods, or improved catalysts.