Abstract The root system of plants derives all its energy from photosynthate translocated from the canopy to the root system. Canopy manipulations that alter either the rate of canopy photosynthesis or the translocation of photosynthate are expected to alter dry matter partitioning to the root system. Field studies were conducted to evaluate the effect of trunk girdling (2008 and 2009) and summer pruning (2009) on soil respiration, maximum quantum yield efficiency of photosystem II and leaf carbohydrate content. In apple trees, following trunk girdling there was increased soil respiration in association with a significant rainfall event suggesting rapid release of organic matter and subsequent microbial decomposition of the carbon. Soil respiration rates returned to baseline levels over time. Reduction in midday maximum quantum efficiency of photosystem II (RPSII) was increased by girdling when crop load was low and this reduction was not related to leaf carbohydrate levels. Girdling reduced leaf sucrose and sorbitol levels in both years, however, total leaf carbohydrates were not affected by girdling. Summer pruning increased soil respiration within 2 weeks of treatment in association with a significant rainfall event, also suggesting a release of organic matter and microbial decomposition of the carbon. Cultural practices that severely affect canopy sink source relationships such as girdling and summer pruning increase soil respiration, however these effects appear to be very short lived, 3–10 days, followed by recovery of the soil/root system to similar levels of soil carbon dioxide efflux. These cultural practices do not likely pose a long-term detrimental effect on root system efficiency because the effects are of short duration with apparent recovery.