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Nanosized zinc sulfides (nano-ZnS) have size-dependent and tunable physical and chemical properties that make them useful for a variety of technological applications. For example, structural changes, especially caused by strain, are pronounced in nano-ZnS < 5 nm in size, the size range typical of incidental nano-ZnS that form in the environment. Previous research has shown how natural organic matter impacts the physical properties of nano-ZnS but was mostly focused on their aggregation state. However, the specific organic molecules and the type of functional groups that are most important for controlling the nano-ZnS size and strain remain unclear. This study examined the size-dependent strain of nano-ZnS synthesized in the presence of serine, cysteine, glutathione, histidine, and acetate. Synchrotron total scattering pair distribution function analysis was used to determine the average crystallite size and strain. Among the different organic molecules tested, those containing a thiol group were shown to affect the particle size and size-induced strain most strongly when added during synthesis but significantly reduced the particle strain when added to as-formed nano-ZnS. The same effects are useful to understand the properties and behavior of natural nano-ZnS formed as products of microbial activity, for example, in reducing environments, or of incidental nano-ZnS formed in organic wastes.