Segun your question is very pertinent , as what is the time lag for evaluating the soil organic carbon stock in response to organic fertilizer application . This is exercise needs some kind of pre-evaluation studies , since soil-climate-nature of crop trio will dictate the optimum  time lag. But , this is for sure , the carbon sock of every soil will vary within the potential sink capacity of the soil , called maxima and minima . More important is to transform such changes in carbon stock of soil as irreversible sock of soil , contributing towards active pool of soil carbon to obtain any anticipated response efficiency .

Mr.Segun,we normally collect soil samples after a main long duration crop or after a sequence or rotation of crops preferably in summer where we get more gap between the crop/crops.But it is desired to collect sample immediately after the harvest of crop.One can collect sample initially before starting of experiment, after one year ,then after every 2--3 years to get perceptible changes.If one desires to compute carbon  stock ,sampling need to be done depth wise to cover entire profile.Sampling can be done in winter also between two main crops.

Segun your question is very pertinent , as what is the time lag for evaluating the soil organic carbon stock in response to organic fertilizer application . This is exercise needs some kind of pre-evaluation studies , since soil-climate-nature of crop trio will dictate the optimum  time lag. But , this is for sure , the carbon sock of every soil will vary within the potential sink capacity of the soil , called maxima and minima . More important is to transform such changes in carbon stock of soil as irreversible sock of soil , contributing towards active pool of soil carbon to obtain any anticipated response efficiency .

Dear Segun, As mentioned by the above researchers, pr-planting and per-fertilization soil analysis is very important, which can be used as a base line to compare with subsequent C content results. One important point raised by Dr.  Rao is soil depth. Soil C including other nutrient contents of soil vary with soil depth, usually inverse relationship. If the measurement is done along with a sort of field trials, measurement of C even including other nutrients at the mid stage and end point of the trials can also help the residence time of C in the organic resource applied as soil amendment. Because this differs from one to another; for example, C in cereal and legume crop residues, manure, biochar, etc. 

Type and sink capacity of a soil as mentioned by Dr. Anoop , climatic condition and soil moisture content may also affect the status and residence time of the C in soils. Please see the C content of a soil determined at two stages after application in the paper attached here.

It is always desired to sample profile/depth wise  soil samples and compute carbon stocks.We need to measure bulk density of soil also to compute carbon stock.We also need to  plan experiments on carbon stock measurements at least for 4-5 years.Long-term experiments are better option.All carbon inputs better be applied on carbon basis for comparison.

Very good suggestions have been made by Dr. Rao and Dr. Anoop and supplemented by Agegnehu. The decomposition of applied organic matter depends upon climatic conditions and total microbial population in a soil in addition to moisture conditions. When your are documenting OM status changes you have to analyse the soil after harvesting of each crop in the sequence, if growing crops is a component of your study. If crops are not included in the objective and you want to investigate changes in soil then analysis of soil after every 2-3 months may be useful, though this duration can be extended to four months in winter. However, as pointed out by Dr. Rao, sampling depth is also very important and you may need to sample up to 60 cm or so.