Recently, inducing the formation of conductive magnetite-embedded granules (MEGs) by self-embedding submicron magnetite particles into anaerobic granules has been demonstrated to be effective in enhancing methanation and improving sludge stability in upflow anaerobic sludge blanket (UASB) reactors. However, MEGs still suffer structural and functional destabilization at high organic loading rates (OLRs) due to the excessive secretion of extracellular polymeric substances (EPS), resulting in a significant washout of active microbes. This is particularly true when treating carbohydrate-rich wastewater that is prone to producing excessive EPS. In order to address this issue, this study explored the potential of combining MEG-UASB process with feed pre-acidification as a means of improving the methanogenic treatment performance and stability of whey, a carbohydrate-rich dairy effluent. Two UASB reactors, one with MEGs and one without, were operated to treat pre-acidified whey at increasing OLRs of 2–11 g chemical oxygen demand/L·d. Feed pre-acidification was effective in preventing granule destabilization and maintaining stable UASB performance with or without MEGs. Meanwhile, the reactor with MEGs (JM) showed significantly better performance and stability than the one without MEGs (JC), especially at high OLRs, which was likely because MEGs improved sludge retention and promoted electro-syntrophic methanogenic activity. Accordingly, JM sludge exhibited greater electron transfer capability and a more pronounced enrichment of electroactive microbes than JC sludge. External voltage application (0.6 V) did not relieve but rather aggravated the process upset under overloading conditions for both reactors. The overall results suggest that the MEG-UASB process coupled with pre-acidification holds promise for efficient and stable treatment of carbohydrate-rich wastewater.