Environmental exposures to agrochemicals and nutritional factors may be associated with Parkinson’s Disease (PD). None of the studies to date has examined the combined effects of diet and agricultural chemical exposure together. To address these research gaps, we aimed to assess the association of nutritional factors and agrochemical exposure with the risk of PD. A hospital-based case-control study was conducted. Multivariable logistic regressions were used to estimate the association of nutritional and agrochemical exposures with PD, adjusting for gender, age, socio-economic status, head injury, family history, smoking, metals exposure, and α-synuclein gene polymorphism. Weighted Quantile Sum (WQS) regression was applied to examine the effect of dietary components as a mixture. We recruited 347 cases and 389 controls. Parent history of PD (OR = 4.15, 95%CI: 2.10, 8.20), metals exposure (OR = 2.50, 95%CI: 1.61–3.89), SNCA rs356219 polymorphism (OR = 1.39, 95%CI: 1.04–1.87 for TC vs. TT; OR = 2.17, 95%CI: 1.43–3.28 for CC vs. TT), agrochemical exposures (OR = 2.11, 95%CI: 1.41–3.16), and being born in the Brescia province (OR = 1.83, 95%CI: 1.17–2.90) were significantly associated with PD. Conversely, fish intake and coffee consumption had a protective effect. The study confirmed the role of environmental exposures in the genesis of PD. Fish intake and coffee consumption are protective factors even when agricultural chemical exposures exist. Genetic factors and metals exposure were confirmed as risk factors for PD.