The aim of the present study was to determine whether arbuscular mycorrhizal (AM) inoculation with a biofertilizer containing clays as granular carriers, leek root pieces and Glomus intraradices spores could improve alkalinity tolerance of two cucumber genotypes, and to study the changes induced by AM at agronomical and physiological level. A greenhouse experiment was carried out to determine yield, growth, fruit quality, net photosynthesis (ACO2), electrolyte leakage, and mineral composition of two cucumber (Cucumis sativus L.) genotypes (hybrid “Ekron” or open-pollinated variety “Marketmore”) with inoculated and noninoculated arbuscular mycorrhizal biofertilizer. Plants were supplied with nutrient solutions at two pH values (6.0 or 8.1). The high pH nutrient solution had the same basic composition with an additional 10 mM NaHCO3 and 0.5 gl−1 CaCO3. The percentage root colonization was higher in “Marketmore” (21.8%) than “Ekron” (12.7%). Total and marketable yield and total biomass were significantly higher by 189%, 213%, and 77%, respectively, with Ekron in comparison to those recorded with Marketmore. The highest crop performance with Ekron in comparison to Marketmore was due to the improved nutritional status (higher N, P, K, Ca, Mg, Fe, Mn, and B), higher leaf area, and net photosynthesis. Increasing the concentration of NaHCO3 from 0 to 10 mM in the nutrient solution significantly decreased yield, plant growth, ACO2, N, P, Fe, Cu, Zn, Mn, and B concentration inleaf tissue, whereas the electrolyte leakage increased. The inoculated plants under alkaline conditions had higher total, marketable yield, and total biomass than noninoculated plant. Mycorrhizal cucumber plants grown under alkaline conditions had a higher macronutrient concentration in leaf tissue compared to noninoculated plants. The highest yield and biomass production in inoculated plants seems to be related to the capacity of maintaining higher net ACO2 and to a better nutritional status (high P, K, Mg, Fe, Zn, and Mn and low Na accumulation) in response to bicarbonate stress with respect to AM plants.