This study aimed to compare the effects of 1 × 1 small-sided games (SSGs) with different bout durations on external (ETL) and internal training loads (ITL) in youth soccer players. Twenty U18 players were divided into two groups performing six 1 × 1 SSGs with 30 and 45 s bout durations on a playing field of 10 by 15 m. ITL indices, including the percentage of maximum heart rate (HR), blood lactate (BLa) level, pH, bicarbonate (HCO3−) level, and base excess (BE) level, were measured at rest, after each SSG bout, and 15 and 30 min after the entire exercise protocol. ETL (Global Positioning System metrics) was recorded during all six SSG bouts. The analysis showed that the 45 s SSGs had a greater volume (large effect) but a lower training intensity (small to large effect) than the 30 s SSGs. A significant time effect (p < 0.05) was observed in all ITL indices and a significant group effect (F1, 18 = 8.84, p = 0.0082, ƞ2 = 0.33) in the HCO3− level only. Finally, the changes in the HR and HCO3− level were smaller in the 45 s SSGs than in the 30 s SSGs. In conclusion, 30-s games, characterized by a higher intensity of training effort, are more physiologically demanding than 45-s games. Secondly during short-bout SSG training the HR and BLa level have limited diagnostic value for ITL. Extending ITL monitoring using other indicators, such as the HCO3− and BE levels, appears reasonable.