The total number of seats won by each one of the six qualifying parties is the minimum number of mandates the party would be entitled to receive at the federal level. The number of second votes won by each qualifying party would then be divided by its corresponding seat total from the preceding allocation, minus 0.5:

The votes-to-seats minus 0.5 quotients show a significant deviation from full proportionality - with quotients ranging from a low of 60,813 for CDU to a high of 69,790 for FDP - largely due to the allocation of twenty-six overhang mandates (22 CDU, 3 CSU and one SPD). The distribution of seats on a Land-by-Land basis would have also introduced a distorting effect, but it would have been comparatively minuscule: had overhang seats been disregarded at this stage, the quotients would have fluctuated between 67,784 and 69,790.

At any rate, in the second stage the number of second votes polled by each one of the qualifying parties would have been divided by the smallest of the aforementioned quotients, with remainders larger than 0.5 rounded up to the next whole number, to obtain the definitive nationwide distribution of Bundestag seats:

This would conclude the allocation of seats at the federal level, and the mandates obtained by each party would then be distributed among its Land lists; the results of the initial Land-level allocation of seats would be discarded at this point.

Under the previous electoral system, party mandates were proportionally allocated among its Land lists, but if a Land list received fewer seats than its corresponding number of direct mandates, it kept the overhang seats, and the size of the Bundestag was increased accordingly. However, under the new electoral system, the allocation of Bundestag seats at the federal level is definitive and cannot be altered by the distribution of party mandates at the Land level. As such, in the event one or more party Land lists receive fewer seats than the corresponding number of constituency seats won by the party, the allocation divisor would be increased until each one of the party's Land lists received a number of seats equal to the larger of its rounded quotient, or its corresponding number of direct mandates.

Nonetheless, in most cases all the Land lists of a given party secure a proportional allocation larger than or equal to their corresponding number of constituency seats, and in such instances the system remains essentially unchanged from past Bundestag elections, the main difference being the actual PR method used for the distribution of seats (d'Hondt from 1957 to 1983, Hare/Niemeyer from 1987 to 2005, Sainte-Laguë/Schepers since 2009). For example, the Land-level allocation of SPD mandates according to the Sainte-Laguë/Schepers method would have produced the following results (with a divisor of 60,541):

As in past elections, any direct mandates won by a party in a particular Land would be deducted from its proportional seat allocation. Thus, the 27 constituency seats won by SPD in Nordrhein-Westfalen would be subtracted from its proportional allocation of 44 seats, and the party would be awarded seventeen list seats in that Land.

However, in the case of CDU the number of constituency seats won by the party would exceed its Land list seat allocation in several Länder, which would require the allocation divisor to be increased from 60,658 to 68,400, with the following results:

Thus, party Land lists still retain their corresponding overhang mandates (if any), but now these will be proportionally deducted from the party's lists in the remaining Länder.

The final distribution of seats in the 2009 Bundestag election would have then stood as follows:

While the new electoral system would have increased the size of the Bundestag by 49 seats, to a total of 671, it would not have substantially changed the outcome of the 2009 Bundestag election: incumbent Chancellor Angela Merkel would still have been able to form a CDU/CSU-FDP coalition government, albeit with a parliamentary majority cut in half (from 332-290 to 346-325) when compared to the actual election outcome.