Membranes are ubiquitous structures in cells. The effects of membranes on various functional molecules have been reported, but their behaviors under macromolecular crowding and cell-sized confinement have not fully been understood. In this study, we model an intracellular environment by crowding micrometer-sized droplets and investigate the effects of membrane properties on molecular diffusion. The molecular diffusion inside small droplets covered with a lipid layer of phosphatidylcholine (PC) becomes slower compared with that of the corresponding bulk solutions under a crowding condition of polysaccharide dextran but not of its monomer unit, glucose. The addition of a poly(ethylene glycol) conjugated lipid (PEGylated lipid) to the PC membrane significantly alters the degree of slow diffusion observed inside small droplets of concentrated dextran. Interestingly, the change is not monotonic against dextran concentration; that is, the PEGylated membrane increases and decreases the degree of slow diffusion with increasing dextran concentration. We explain the nonmonotonic alternation from the increase in effective dextran concentration and the hindered temporal adsorption of dextran to the membrane. Because diffusion alteration by adding PEGylated lipid is observed for condensed small droplets of linear polymer PEG and hydrophilic protein bovine serum albumin, the phenomenon is general for other polymer systems as well. Furthermore, our findings may facilitate the understanding of intracellular molecular behaviors based on membrane effects as well as the development of numerous applications using polymer droplets.