Strategy I plants may respond to iron (Fe) deficiency by rhizosphere acidification. Here, the role of medium pH-values in silicon (Si)-induced mitigation Fe deficiency in Strategy I plants (Cucumis sativus) was investigated, particularly the metabolites regulated by a lack of Fe, using a target metabolomics approach. Plants were grown hydroponically, either with (+Fe) or in Fe-free (−Fe) nutrient solution, with (+Si) or without (−Si) a Si supply. The nutrient solution was adjusted to pH 5.0 or 6.0 and checked daily. Leaf metabolites potentially involved in Fe transport were determined. The typical Fe responses of cucumber (e.g., decrease in leaf chlorophyll, Fe imbalance) were more pronounced when plants were grown at pH 6.0 than 5.0, during long-term Fe deficiency (15 days). Major metabolites up-regulated by Fe deficiency and found in young leaf were succinic, citric and glutamic acids, respectively; their maximal concentrations occurred in Fe-starved plants grown at pH 6.0 without Si supply. Silicon (Si)-induced effects accompanied with alleviation chlorosis symptoms, were most distinct in plants grown at pH 6.0 for an extended period without Fe. Changes in abundance of metabolites specifically up-regulated by a lack of Fe may be manifested before any Si-induced changes in plant Fe content were apparent, suggesting that metabolite responses are highly sensitive to a Fe-dependent signal altered by Si treatments under Fe deficiency. The results indicate that Si supply was more evident when plants were more stressed by an increase in nutrient solution pH under Fe-limited conditions.