Cre-mediated recombineering is the main tool of choice for cell type-specific analysis of gene function in pre-clinical models. In the type 1 diabetes research field, multiple lines of NOD mice have been generated that express Cre in pancreatic β-cells using insulin promoter fragments, but tissue promiscuity remains a concern. The constitutive Ins1tm1.1(cre)Thor (Ins1Cre) mouse on a C57/bl6-J background has been shown to have high β-cell specificity and with no off-target effects reported. Therefore, we explored if Ins1Cre mice on an NOD background could be used as a novel tool to investigate β-cell specific gene deletion in a type 1 diabetes setting. Here, we examine a new NOD mouse model in which Cre is inserted into the endogenous Ins1 locus for ideal β-cell specificity. Fully wildtype (Ins1WT/WT), Ins1 heterozygous (Ins1Cre/WT or Ins1Neo/WT), and Ins1 null mice (Ins1Cre/Neo) littermate mice had either none, one or two Ins1 alleles replaced with Cre or a neomycin cassette. Female Ins1 Neo/WT mice exhibited significant protection from type 1 diabetes. Ins1Cre/WT knock-in mice were further protected. The effects of combined neo and Cre knock-in in Ins1Neo/Cre mice were additive and resulted in near-complete type 1 diabetes prevention up to one year of age. In Ins1Neo/Cre mice, protection from diabetes was associated with reduced in insulitis at 12 weeks of age. We were unable to find significant differences in insulin auto-antibodies or in immune populations between genotypes in the pancreatic lymph node or spleen in 50 weeks old mice, suggesting a β-cell specific mechanism. Collectively, these data confirm previous reports that the loss of Ins1 alleles protects NOD mice from diabetes and demonstrates, for the first time, that Cre itself may have additional protective effects. This has significant implication for the experimental design and interpretation of pre-clinical type 1 diabetes studies using β-cell-specific Cre in NOD mice.